Antibodies that specifically bind to TIM3

ABSTRACT

Provided herein are antibodies specific for TIM3 that can be used to detect cancer cells, in particular, cancer stem cells. The antibodies can also be used in therapeutic compositions for treating cancer and reducing inflammation.

CROSS-REFERENCES TO RELATED APPLICATIONS

The present application claims priority to U.S. Provisional Application No. 61/504,062, filed Jul. 1, 2011, and U.S. Provisional Application No. 61/660,530, filed Jun. 15, 2012, the disclosures of which are incorporated herein by reference in their entireties.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE

The Sequence Listing written in file -27-2.TXT, created on Aug. 28, 2012, 77,824 bytes, machine format IBM-PC, MS-Windows operating system, is hereby incorporated by reference in its entirety for all purposes.

BACKGROUND OF THE INVENTION

T cell immunoglobulin and mucin domain-containing molecule 3 (TIM3) is an immunoglobulin (Ig) superfamily member, expressed on Th1 cells. TIM3 has been shown to play a role in modulating the immune response of Th1 cells, and reducing inflammation in a number of conditions.

TIM3 is also expressed on cancer cells, and on cancer stem cells (CSCs), which are cells that can give rise to additional cancer cells.

One of the major limitations of chemotherapy is the general inability of anticancer drugs to discriminate between normal and cancer cells. Almost all members of the major categories of antineoplastic agents have considerable toxicity for normal cells.

Compositions that specifically target cancer cells can avoid this problem. However, existing cancer targets do not target CSCs. For this reason, existing chemotherapeutic strategies, even when specifically delivered to cancer cells, do not effectively eliminate the cancer. Risk of recurrence remains because the surviving CSCs can give rise to new cancer cells.

Provided herein are anti-TIM3 antibodies that are rapidly internalized into TIM3 expressing cells. These antibodies provide novel diagnostic and therapeutic strategies for targeting TIM3-associated disorders.

BRIEF SUMMARY OF THE INVENTION

Provided herein are TIM3-specific antibodies with improved properties, e.g., for targeting cancer cells, reducing cancer cell growth, and reducing inflammation due to CD4 T cells. In some embodiments, the invention provides an isolated antibody that specifically binds the extracellular domain of TIM3 (a TIM3-specific antibody), wherein said binding results in internalization into a TIM3-expressing cell. In some embodiments, the TIM3-specific antibody is linked to a cytotoxic agent. In some embodiments, the cytotoxic agent is selected from saporin, a taxane, a vinca alkaloid, an anthracycline, and cisplatin.

In some embodiments, the TIM3-expressing cell (in which the TIM3-specific antibody is internalized) is a cancer stem cell (CSC). In some embodiments, the TIM3-expressing cell is a hematopoietic cancer cell, e.g., a lymphoma such as a B cell lymophoma, T cell lymphoma, Burkitt's lymphoma, Hodgkin's lymphoma, or non-Hodgkin's lymphoma. In some embodiments, the hematopoietic cancer cell is from a leukemia or myeloma, e.g., acute myelogenous leukemia (AML), acute lymphoblastic leukemia (ALL), chronic myelogenous leukemia (CML), chronic lymphoblastic leukemia (CLL), Chronic Myelomonocytic Leukemia (CMML), Myelodysplastic Syndrome (MDS), etc. In some embodiments, the TIM3-expressing cell is a solid tumor cell from, e.g., colon cancer, ovarian cancer, liver cancer, prostate cancer, uterine cancer, breast cancer, or renal cancer.

In some embodiments, at least 50% of the TIM3-specific antibody is internalized in 20 minutes in appropriate conditions as described herein (e.g., at appropriate temperature (e.g., 20-37° C.), accounting for antibody concentration relative to cell numbers, etc.). In some embodiments, the TIM3-specific antibody is internalized at a higher rate than the 2E2 antibody.

In some embodiments, the internalizing TIM3-specific antibody can bind a TIM3-expressing cell, wherein said binding inhibits proliferation of the TIM3-expressing cell. In some embodiments, the internalizing TIM3-specific antibody binds a higher percentage of peripheral blood mononuclear cells (PBMCs) from an individual having a hematopoietic cell cancer than the anti-TIM3 antibody 2E2. In some embodiments, the internalizing TIM3-specific antibody can mediate complement dependent cytotoxicity (CDC), e.g., such that more than 10, 20, 30, 40, 50% or higher percentage of TIM3 expressing cells in a sample are killed by CDC within 1 hour under appropriate conditions as described herein (e.g., with functional complement proteins, at appropriate temperature, accounting for antibody concentration relative to amount of complement and cell numbers, etc.). In some embodiments, the internalizing TIM3-specific antibody does not mediate CDC, e.g., less than 10% of TIM3 expressing cells in a sample are killed by CDC within 1 hour under appropriate conditions. In some embodiments, the internalizing TIM3-specific antibody can inhibit release of an inflammatory cytokine from an activated CD4+ T cell, compared to the release of the inflammatory cytokine in the absence of the antibody.

In some embodiments, the internalizing TIM3-specific antibody competes for binding with a competitor antibody selected from the group consisting of:

-   -   an antibody having light chain complementarity determining         region (CDR) sequences of SEQ ID NOs:8-10 and heavy chain CDR         sequences of SEQ ID NOs:3-5 (1.7E10);     -   an antibody having light chain CDR sequences of SEQ ID NOs:18-20         and heavy chain CDR sequences of SEQ ID NOs:13-15 (7.10F6);     -   an antibody having light chain CDR sequences of SEQ ID NOs:28-30         and heavy chain CDR sequences of SEQ ID NOs:23-25 (8.16C10);     -   an antibody having light chain CDR sequences of SEQ ID         NOs:108-110 and heavy chain CDR sequences of SEQ ID NOs:103-105         (27.12E12); and     -   an antibody having light chain CDR sequences of SEQ ID         NOs:118-120 and heavy chain DR sequences of SEQ ID NOs: 113-115         (9.1G12).

In some embodiments, the internalizing TIM3-specific antibody is selected from the group consisting of the above competitor antibodies. In some embodiments, the internalizing TIM3-specific antibody comprises the heavy and light chain CDR sequences of 1.7E10. In some embodiments, the internalizing TIM3-specific antibody comprises the heavy and light chain CDR sequences of 7.10F6. In some embodiments, the internalizing TIM3-specific antibody comprises the heavy and light chain CDR sequences of 8.16C10. In some embodiments, the internalizing TIM3-specific antibody comprises the heavy and light chain CDR sequences of 27.12E12. In some embodiments, the internalizing TIM3-specific antibody comprises the heavy and light chain CDR sequences of 9.1G12.

In some embodiments, the internalizing TIM3-specific antibody is selected from the group consisting of:

-   -   an antibody having a light chain variable region sequence         comprising SEQ ID NO:7 and a heavy chain variable region         sequence of SEQ ID NO:2 (1.7E10);     -   an antibody having a light chain variable region sequence         comprising SEQ ID NO:17 and a heavy chain variable region         sequence comprising SEQ ID NO:12 (7.10F6);     -   an antibody having a light chain variable region sequence         comprising SEQ ID NO:27 and a heavy chain variable region         sequence comprising SEQ ID NO:22 (8.16C10);     -   an antibody having a light chain variable region sequence         comprising SEQ ID NO:107 and a heavy chain variable region         sequence comprising SEQ ID NO:102 (27.12E12); and     -   an antibody having a light chain variable region sequence         comprising SEQ ID NOs:117 and a heavy chain variable region         sequence comprising SEQ ID NO:112 (9.1G12).

Internalizing TIM3-specific antibodies can be used in methods of treating cancer, including but not limited to killing cancer cells using the internalizing TIM3-specific antibody linked to a cytotoxic agent. The internalizing TIM3-specific antibody can be formulated in a pharmaceutical composition. In some embodiments, the method comprises contacting a TIM3 expressing cancer cell with the internalizing TIM3-specific antibody. In some embodiments, the TIM3 expressing cancer cell is a hematopoietic cancer cell (e.g., lymphoma, leukemia, myeloma, and subsets thereof described herein). In some embodiments the TIM3 expressing cancer cell is a cancer stem cell. In some embodiments, the TIM3 expressing cancer cell is from a solid tumor, including but not limited to cells from colon cancer, ovarian cancer, liver cancer, prostate cancer, uterine cancer, breast cancer, and kidney cancer. In some embodiments, the contacting comprises administering the internalizing TIM3-specific antibody to an individual having a TIM3-expressing cancer as described herein.

Further provided are TIM3-specific antibodies that specifically bind to the extracellular domain of TIM3 and inhibit proliferation of TIM3-expressing cells upon binding, e.g., compared to proliferation in the absence of the antibody. In some embodiments, the proliferation inhibiting TIM3-specific antibody (or TIM3-binding portion thereof) is crosslinked, e.g., to a solid or semisolid matrix (e.g., a bead). In some embodiments, the proliferation inhibiting TIM3-specific antibody (or TIM3-binding portion thereof) is multimerized, e.g., linked to each other, in a multivalent antibody, or multivalent antibody isotype (e.g., IgM or IgA).

In some embodiments, the TIM3 expressing cancer cell is a hematopoietic cancer cell (e.g., lymphoma, leukemia, myeloma, and subsets thereof described herein). In some embodiments, the TIM3 expressing cancer cell is a cancer stem cell. In some embodiments, the TIM3 expressing cancer cell is from a solid tumor, e.g., selected from the group consisting of colon cancer, ovarian cancer, liver cancer, prostate cancer, uterine cancer, breast cancer, and kidney cancer.

In some embodiments, the proliferation inhibiting TIM3-specific antibody is selected from the group consisting of:

-   -   an antibody comprising the CDR sequences of 1.7E10 (CDRH1-3=SEQ         ID NOs:3-5; CDRL1-3=SEQ ID NOs:8-10); and     -   an antibody comprising the CDR sequences of 7.10F6 (CDRH1-3=SEQ         ID NOs:13-15; CDRL1-3=SEQ ID NOs:18-20).

In some embodiments, the proliferation inhibiting TIM3-specific antibody is selected from the group consisting of:

-   -   an antibody comprising variable region sequences of 1.7E10         (V1=SEQ ID NO: 7; Vh=SEQ ID NO:2); and     -   an antibody having variable region sequences of 7.10F6 (V1=SEQ         ID NO:17; Vh=SEQ ID NO:12).

In some embodiments, the proliferation inhibiting TIM3-specific antibody is conjugated to (linked to) a cytotoxic agent. In some embodiments, the proliferation inhibiting TIM3-specific antibody is not linked to a cytotoxic agent. In some embodiments, the TIM3-specific antibody is conjugated to a detectable agent. In some embodiments, the antibody is formulated into a pharmaceutical composition.

In some embodiments, the proliferation inhibiting TIM3-specific antibodies can be used in methods for treating cancer. In some embodiments, the method comprises contacting a TIM3 expressing cancer cell (e.g., as described above) with the proliferation inhibiting TIM3-specific antibody. In some embodiments, the contacting comprises administering the proliferation inhibiting TIM3-specific antibody to an individual, e.g., an individual having a TIM3-expressing cancer. In some embodiments, the proliferation inhibiting TIM3-specific antibody is cross-linked or multimerized prior to administration.

In some embodiments, the TIM3-specific antibody that reduces (inhibits) TIM3-expressing cell proliferation also is internalized into TIM3-expressing cells. In some embodiments, the TIM3-specific antibody that reduces TIM3-expressing cell proliferation also mediates CDC. In some embodiments, the proliferation inhibiting TIM3-specific antibody does not mediate CDC. In some embodiments, the TIM3-specific antibody that reduces TIM3-expressing cell proliferation also reduces release of an inflammatory cytokine from an activated T cell, e.g., compared to release of the inflammatory cytokine in the absence of the antibody.

In some embodiments, the proliferation inhibiting TIM3-specific antibody binds a higher percentage of PBMCs or BMMCs from an individual having a hematopoietic cell cancer (e.g., AML or B cell lymphoma) than 2E2. For example, the TIM3-specific antibody can bind more than 2%, 5%, 8%, 10%, or higher percentage of PBMCs or BMMCs from an individual having leukemia or lymphoma (e.g., a primary patient sample).

Further provided are antibodies that specifically bind the extracellular domain of TIM3, wherein the antibody binds a high percentage of PBMCs or BMMCs from an individual having a hematopoietic cell cancer with high intensity (e.g., as determined by brighter staining by FACS). In some embodiments, the TIM3-specific antibody binds a higher percentage of PBMCs or BMMCs than the anti-TIM3 antibody 2E2 (and can be referred to as a “high hematopoietic cancer cell binding TIM3-specific antibody”). In some embodiments, the hematopoietic cell cancer is selected from lymphoma (e.g., Burkitt's lymphoma, B cell lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma); leukemia (e.g., an acute or chronic leukemia, or pre-leukemia such as myelodysplastic syndrome, chronic myelomonocytic leukemia, etc.); and myeloma (e.g., AML, CML, etc.).

In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody binds at least 3%, 5%, 8%, 10%, 12%, 15%, 20% or higher % of the PBMCs from the individual. In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody is linked to a detectable label. In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody is linked to a cytotoxic agent.

In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody competes for binding with a competitor antibody selected from:

-   -   an antibody comprising light chain CDR sequences of SEQ ID         NOs:8-10 and heavy chain CDR sequences of SEQ ID NOs:3-5         (1.7E10);     -   an antibody comprising light chain CDR sequences of SEQ ID         NOs:18-20 and heavy chain CDR sequences of SEQ ID NOs:13-15         (7.10F6);     -   an antibody comprising light chain CDR sequences of SEQ ID         NOs:108-110 and heavy chain CDR sequences of SEQ ID NOs:103-105         (27.12E12); and     -   an antibody comprising light chain CDR sequences of SEQ ID         NOs:118-120 and heavy chain CDR sequences of SEQ ID NOs: 113-115         (9.1G12).

In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody comprises the CDR sequences or the variable region sequences of 1.7E10. In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody comprises the CDR sequences or the variable region sequences of 7.10F6. In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody comprises the CDR sequences or the variable region sequences of 27.12E12. In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody comprises the CDR sequences or variable region sequences of 9.1G12.

The high hematopoietic cancer cell binding TIM3-specific antibodies can be used for diagnosing a hematopoietic cancer in an individual, e.g., where the antibody is linked to a detectable label. In some embodiments, the method of diagnosis can comprise contacting a high hematopoietic cancer cell binding TIM3-specific antibody with a biological sample from an individual, and determining binding of the antibody to cells in the biological sample, wherein binding indicates that the individual has hematopoietic cell cancer. In some embodiments, the sample is blood or a blood fraction. In some embodiments, the method comprises administering a high hematopoietic cancer cell binding TIM3-specific antibody to an individual and determining binding of the antibody to cells in the individual wherein binding indicates that the individual has hematopoietic cell cancer. In this in vivo diagnostic method, the hematopoietic cancer can be also be localized in the individual.

In some embodiments, the method further comprises treating the individual for hematopoietic cell cancer, i.e., where the determining step indicates that the individual has a hematopoietic cell cancer. Thus, in some embodiments, the method further comprises administering a chemotherapeutic agent to the individual. In some embodiments, the chemotherapeutic agent comprises the same high hematopoietic cancer cell binding TIM3-specific antibody that was used for the contacting (detecting) step. In some embodiments, the chemotherapeutic agent comprises a high hematopoietic cancer cell binding TIM3-specific antibody that is not the antibody used for the contacting step. In some embodiments, the chemotherapeutic agent comprises a TIM3-specific antibody that competes for binding to TIM3 with a competitor antibody comprising the CDR sequences of an antibody selected from the group consisting of 1.7E10, 7.10F6, 8.16C10, 27.12E12, and 9.1G12. In some embodiments, the chemotherapeutic agent comprises a TIM-3 specific antibody comprising the CDR sequences of an antibody selected from the group consisting of 1.7E10, 7.10F6, 8.16C10, 27.12E12, and 9.1G12. In some embodiments, the chemotherapeutic agent comprises a TIM3-specific antibody comprising the variable region sequences of an antibody selected from the group consisting of 1.7E10, 7.10F6, 8.16C10, 27.12E12, and 9.1G12. In some embodiments, the chemotherapeutic agent comprises a cytotoxic agent, e.g., linked to a TIM3-specific antibody.

The high hematopoietic cancer cell binding TIM3-specific antibodies can be used for methods of treating hematopoietic cell cancers. In some embodiments, the method of treatment can comprise administering a high hematopoietic cancer cell binding TIM3-specific antibody to an individual, thereby treating the hematopoietic cell cancer in the individual. In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody is linked to a cytotoxic agent. In some embodiments, the high hematopoietic cancer cell binding TIM3-specific antibody is cross-linked or multimerized prior to administration. In some embodiments, the method of treatment is combined with the diagnostic method, so that individuals having a hematopoietic cell cancer that displays an epitope that is well-recognized by a particular TIM3-specific antibody, as determined in the diagnostic method, are treated with the same antibody. In this way, the cancer cells in that individual can be more effectively targeted, e.g., than in a non-targeted, or non-individualized, therapeutic method. In this context, the term “well-recognized” indicates that a high percentage of PBMC or BMMC from the individual are bound by the TIM3-specific antibody, e.g., greater than 5%, 10%, 12%, 15%, 20% or more, or that the TIM3-specific antibody binds with high intensity, e.g., higher intensity than the 2E2 antibody as determined by FACS.

In some embodiments, the invention provides an isolated antibody specific for the extracellular domain of TIM3, wherein said antibody competes for binding to TIM3 with a competitor antibody comprising the CDR sequences of an antibody selected from 1.7E10, 7.10F6, 8.16C10, 27.12E12, 27.12A6, 27.2H4, 9.1G12, 6.16F9, 6.14B9, 33.1G12, 33.2A5, and 33.14A5 (see the sequence listing). In some embodiments, the TIM3-specific antibody competes for binding to TIM3 with a competitor antibody selected from the group consisting of 1.7E10, 7.10F6, 8.16C10, 27.12E12, 27.12A6, 27.2H4, 9.1G12, 6.16F9, 6.14B9, 33.1G12, 33.2A5, and 33.14A5. In some embodiments, the TIM3-specific antibody binds the same epitope on TIM3 as an antibody selected from 1.7E10, 7.10F6, 8.16C10, 27.12E12, 27.12A6, 27.2H4, 9.1G12, 6.16F9, 6.14B9, 33.1G12, 33.2A5, and 33.14A5. In some embodiments, the TIM3-specific antibody comprises the variable region sequences of an antibody selected from 1.7E10, 7.10F6, 8.16C10, 27.12E12, 27.12A6, 27.2H4, 9.1G12, 6.16F9, 6.14B9, 33.1G12, 33.2A5, and 33.14A5. In some embodiments, the TIM3-specific antibody is conjugated to a detectable label. In some embodiments, the TIM3-specific antibody is conjugated to a cytotoxic agent. In some embodiments, the TIM3-specific antibody is formulated in a pharmaceutical composition.

In some embodiments, the TIM3-specific antibody is used in a method for detecting the presence of a cancer cell, wherein the method comprises contacting any one of the TIM3-specific antibodies described herein with a plurality of cells and determining whether the TIM3-specific antibody binds to a cell in the plurality of cells, wherein binding indicates that the cell is a cancer cell. In some embodiments, the plurality of cells are in a biological sample from an individual and the method is practiced in vitro. In some embodiments, the plurality of cells are in an individual and the method is practiced in vivo. In some embodiments, the TIM3-specific antibody is conjugated to a detectable label. In some embodiments, the cancer cell is a cancer stem cell (CSC). In some embodiments, the cancer cell is a lymphoma cell (e.g., B cell, Hodgkin's, or Burkitt's lymphoma). In some embodiments, the cancer cell is a myeloma or leukemia cell (e.g., AML, CMML, CML). In some embodiments, the cancer cell is a solid tumor cell (e.g., from colon, ovarian, hepatic, prostate, renal, uterine, or breast cancer). In some embodiments, the method further comprises administering a chemotherapeutic agent to the individual.

Further provided are TIM3 specific antibodies that specifically bind the extracellular domain of TIM3, wherein the TIM3 specific antibody mediates complement dependent cytotoxicity (CDC). In this case, the TIM3-specific antibody is typically administered to an individual diagnosed with, or at risk of developing, cancer, wherein the individual has a functional complement system. In some embodiments, the TIM3-specific antibody is a chimeric antibody, e.g., comprising a human Fc region when the recipient of the TIM3-specific antibody is human. In some embodiments, the TIM3-specific antibody mediates CDC in at least 20% of the TIM3-expressing cells in a population under conditions appropriate for CDC. In some embodiments, the TIM3 specific antibody is selected from the group consisting of:

-   -   an antibody comprising the CDR sequences of 1.7E10 (CDRH1-3=SEQ         ID NOs:3-5; CDRL1-3=SEQ ID NOs:8-10);     -   an antibody comprising the CDR sequences of 7.10F6 (CDRH1-3=SEQ         ID NOs:13-15; CDRL1-3=SEQ ID NOs:18-20);     -   an antibody having the CDR sequences of 8.16C10 (CDRH1-3=SEQ ID         NOs:23-25; CDRL1-3=SEQ ID NOs:28-30);     -   an antibody having variable region sequences of 1.7E10 (V1=SEQ         ID NO:7; Vh=SEQ ID NO:2)     -   an antibody having variable region sequences of 7.10F6 (V1=SEQ         ID NO:17; Vh=SEQ ID NO:12); and     -   an antibody having variable region sequences of 8.16C10 (V1=SEQ         ID NO:27; Vh=SEQ ID NO:22).

Further provided are antibodies that specifically bind the extracellular domain of TIM3, wherein said binding inhibits release of an inflammatory cytokine from an activated CD4+ T cell, compared to the release of the inflammatory cytokine in the absence of the antibody. In some embodiments, the inflammatory cytokine is IL-6. In some embodiments the inflammatory cytokine is IFN-gamma. In some embodiments, the inflammatory cytokine reducing TIM3 specific antibody reduces release of the inflammatory cytokine (e.g., IL-6 or IFN-gamma) more than the 2E2 antibody.

In some embodiments, the inflammatory cytokine reducing TIM3-specific antibody is selected from the group consisting of:

-   -   an antibody comprising the CDR sequences of 1.7E10 (CDRH1-3=SEQ         ID NOs:3-5; CDRL1-3=SEQ ID NOs:8-10);     -   an antibody comprising the CDR sequences of 7.10F6 (CDRH1-3=SEQ         ID NOs:13-15; CDRL1-3=SEQ ID NOs:18-20);     -   an antibody comprising the CDR sequences of 8.16C10 (CDRH1-3=SEQ         ID NOs:23-25; CDRL1-3=SEQ ID NOs:28-30);     -   an antibody comprising the CDR sequences of 9.1G12 (CDRH1-3=SEQ         ID NOs:113-115; CDRL1-3=SEQ ID NOs:118-120);     -   an antibody comprising variable region sequences of 1.7E10         (V1=SEQ ID NO:7; Vh=SEQ ID NO:2)     -   an antibody comprising variable region sequences of 7.10F6         (V1=SEQ ID NO:17; Vh=SEQ ID NO:12);     -   an antibody comprising variable region sequences of 8.16C10         (V1=SEQ ID NO:27; Vh=SEQ ID NO:22);     -   an antibody comprising variable region sequences of 9.1G12         (V1=SEQ ID NO:117; Vh=SEQ ID NO:112).

In some embodiments, the TIM3-specific antibody is used in a method for reducing the release of inflammatory (e.g., Th1) cytokines from CD4+ T cells, wherein the method comprises contacting any one of the TIM-3 specific antibodies described herein with a CD4+ T cell (e.g., a CD4+ T cell prior to activation or an activated CD4+ T cell). The reduction is typically determined by reference to a control, e.g., the release of inflammatory cytokines before contact with the TIM3-specific antibody, or in a sample or individual not treated with the TIM3-specific antibody. In some embodiments, the inflammatory cytokine is interferon-gamma (IFN-gamma). In some embodiments, the inflammatory cytokine is IL-6. In some embodiments, the method is carried out in vitro. In some embodiments, the method is carried out in vivo, and the contacting comprises administering the selected TIM3-specific antibody to an individual with an inflammatory condition (e.g., chronic inflammation, over-recruitment or over-activation of leukocytes or macrophages, autoimmunity, multiple sclerosis, rheumatoid arthritis, type I diabetes, Crohn disease, atherosclerosis, allergic conditions (e.g., allergic encephalomyelitis, asthma), and glomerulonephritis).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. TIM3-specific antibodies do not stain the majority of mature peripheral blood cells. Peripheral blood mononuclear cells (PBMCs) obtained from a normal donor were stained for various hematopoietic lineage markers and either the 1.7E10 antibody or isotype control.

FIG. 2. The presently disclosed TIM3-specific antibodies bind more PBMCs from AML patients at a higher level than commercially available 2E2 antibody. PBMCs were stained with the indicated antibody and gated for live cells. The negative controls were negative for staining (goat anti-mouse IgG (GaMsIgG) and mouse IgG1 (msIgG1)).

FIG. 3. The presently disclosed TIM3-specific antibodies are internalized into TIM3 expressing Pfeiffer cells at a high level. Results for isotype controls are indicated in the first three lanes, for the commercially available 2E2 antibody in lane 4, and for the presently disclosed antibodies in lanes 5-16.

FIG. 4. TIM3-specific antibodies conjugated with saporin effectively kill TIM3-expressing Pfeiffer cells. SAZAP=strepavidin-saporin; Antibody-Biotin=biotin conjugated antibody; Antibody-BZAP=biotinylated, saporin conjugated antibody.

FIG. 5. The presently disclosed TIM3-specific antibodies inhibit proliferation of TIM3-expressing leukemia cells (CMK AML cell line) in cross-linking conditions. The indicated antibodies were plated at various levels (indicated below each set of data) before addition of cells. Relative cell numbers are indicated on the left.

FIG. 6. The presently disclosed TIM3-specific antibodies induce complement dependent cytotoxicity. The variable regions for each indicated antibody (1.7E10, 7.10F6, and 8.16C10) were conjugated to the Fc regions from human antibody. Lysis of TIM3-expressing cells increased in a dose-dependent manner.

FIG. 7. The presently disclosed TIM3-specific antibodies reduce release of Th1 inflammatory cytokines from activated CD4+ T cells. Cytokine levels with the isotype control antibodies were arbitrarily set to 1.0. Addition of the indicated TIM3-specific antibodies to activated T cells reduced IFN-gamma release, and to a lesser extent, reduced IL-6 release.

FIG. 8. TIM3-specific 12E12 antibody shows CDC activity on cells from AML patient samples. (A) shows the intensity of staining denoted by the mean fluorescent intensity (MFI) versus the CDC activity. (B) shows the CDC activity of 12E12 (ms12E12), and was also split into responsive (n=5) and non-responsive (n=6) groups. Data was normalized to IgG control.

DETAILED DESCRIPTION OF THE INVENTION

Provided herein are antibodies specific for the extracellular region of TIM3 and that are rapidly internalized upon binding to a TIM3-expressing cell. In view of this discovery, the internalizing TIM3-specific antibodies can be used to deliver a cytotoxic agent specifically to TIM3-expressing cells, for example, cancer cells such as Cancer Stem Cells (CSC), leukemias, lymphomas, and solid tumor cells.

Also provided are TIM3-specific antibodies that inhibit cancer cell growth in the absence of a cytotoxic agent, e.g., under cross-linked or multimerized conditions. In some embodiments, the present TIM3-specific antibodies further provoke complement dependent cytotoxicity (CDC).

Also provided are TIM3-specific antibodies that are effective for reducing the release of inflammatory cytokines from CD4+ T cells. In addition to, or in combination with the therapeutic applications, the anti-TIM3 antibodies disclosed herein are useful for in vivo and in vitro diagnostic agents.

I. DEFINITIONS

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art. See, e.g., Lackie, DICTIONARY OF CELL AND MOLECULAR BIOLOGY, Elsevier (4^(th) ed. 2007); Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Springs Harbor Press (Cold Springs Harbor, N.Y. 1989). Any methods, devices and materials similar or equivalent to those described herein can be used in the practice of this invention. The following definitions are provided to facilitate understanding of certain terms used frequently herein and are not meant to limit the scope of the present disclosure.

T cell Immunoglobulin- and Mucin domain-containing molecule 3 (TIM3), also known as HAVCR2, KIM-3, TIMD3, and FLJ14428, is a T helper cell type 1-specific cell surface protein that regulates macrophage activation and the severity of inflammatory conditions. TIM3 is also associated with cancer, in particular, with cancer stem cells. The nucleotide and protein sequences of TIM3 are known for many species. For example, the human sequences can be found at Genbank accession number AF251707.1 (SEQ ID NO:121) and Uniprot accession number Q8TDQ0 (SEQ ID NO:122). TIM3 is part of the TIM family of proteins which includes 4 members in mice and at least 3 members in humans. This family of proteins is characterized by an extracellular domain comprising an Ig like domain and a mucin domain (further comprising O-linked and N-linked glycosylation sites), a transmembrane domain, and an intracellular (cytoplasmic) domain. For the human TIM3 protein shown as SEQ ID NO: 122, the extracellular domain comprises approximately amino acids 22-202, the transmembrane domain comprises approximately amino acids 203-223, and the cytoplasmic domain comprises approximately amino acids 224-301. One of skill will understand that TIM3 variants (e.g., species homologs, allelic variants, etc.) can be optimally aligned, e.g., for identification of conserved residues and domains. For review, see Kuchroo et al. (2003) Nature Rev. Immunol. 3:454.

The terms “TIM3-specific antibody,” “anti-TIM3 antibody,” “TIM3 antibody,” and “anti-TIM3” are used synonymously herein to refer to an antibody that specifically binds to TIM3. The TIM3 antibodies described herein specifically bind the TIM3 polypeptide expressed, e.g., on the surface of certain cancer cells (e.g., cancer stem cells (CSCs) or hematopoietic tumor cells (HTCs)), but not to most mature peripheral blood cells. As discussed in more detail below, the present anti-TIM3 antibodies can bind TIM3 expressing cells, inhibit their proliferation and/or mediate their destruction.

A “TIM3-associated disorder” (or TIM3 related disorder, TIM3 disorder, TIM3 related condition or disease, etc.) refers to conditions and diseases correlated with elevated or reduced cell surface expression of TIM3 as compared to TIM3 expression in a standard control (e.g., a normal, non-disease, non-cancer cell). Elevated TIM3 levels are associated with cancer cells, in particular, cancer stem cells.

The terms “internalize,” “internalization,” “endocytose,” “endocytosis,” “engulf,” and like terms refer to uptake of a substance by a cell, e.g., by antibody (or receptor)-mediated endocytosis or phagocytosis.

The terms “engraft” or “engraftment” refers to the ability of a cell to survive, proliferate, and/or properly localize upon introduction into an individual or tissue. In the case of a cancer stem cell (CSC), the term can refer to the ability of the CSC to generate a tumor de novo or to spread to a different site. The term is commonly used to describe the ability of a population of cells to survive and function in a xenograft model (e.g., engraftment of human cells in a mouse). Engraftment of hematopoietic cells can be determined as described, e.g., in WO2006/047569. Engraftment of tumor cells can be determined as described, e.g., in Beckhove et al. (2003) Int. J. Cancer 105:444.

“Nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form, and complements thereof. The term “polynucleotide” refers to a linear sequence of nucleotides. The term “nucleotide” typically refers to a single unit of a polynucleotide, i.e., a monomer. Nucleotides can be ribonucleotides, deoxyribonucleotides, or modified versions thereof. Examples of polynucleotides contemplated herein include single and double stranded DNA, single and double stranded RNA (including siRNA), and hybrid molecules having mixtures of single and double stranded DNA and RNA.

The words “complementary” or “complementarity” refer to the ability of a nucleic acid in a polynucleotide to form a base pair with another nucleic acid in a second polynucleotide. For example, the sequence A-G-T is complementary to the sequence T-C-A. Complementarity may be partial, in which only some of the nucleic acids match according to base pairing, or complete, where all the nucleic acids match according to base pairing.

A variety of methods of specific DNA and RNA measurements that use nucleic acid hybridization techniques are known to those of skill in the art (see, Sambrook, Id.). Some methods involve electrophoretic separation (e.g., Southern blot for detecting DNA, and Northern blot for detecting RNA), but measurement of DNA and RNA can also be carried out in the absence of electrophoretic separation (e.g., quantitative PCR, dot blot, or array).

The words “protein”, “peptide”, and “polypeptide” are used interchangeably to denote an amino acid polymer or a set of two or more interacting or bound amino acid polymers. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers, those containing modified residues, and non-naturally occurring amino acid polymer.

The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function similarly to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, e.g., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs may have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions similarly to a naturally occurring amino acid.

Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.

“Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical or associated, e.g., naturally contiguous, sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode most proteins. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to another of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes silent variations of the nucleic acid. One of skill will recognize that in certain contexts each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, often silent variations of a nucleic acid which encodes a polypeptide is implicit in a described sequence with respect to the expression product, but not with respect to actual probe sequences.

As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention. The following amino acids are typically conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins (1984)).

The terms “identical” or “percent identity,” in the context of two or more nucleic acids, or two or more polypeptides, refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides, or amino acids, that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters, or by manual alignment and visual inspection. See e.g., the NCBI web site at ncbi.nlm.nih.gov/BLAST. Such sequences are then said to be “substantially identical.” This definition also refers to, or may be applied to, the compliment of a nucleotide test sequence. The definition also includes sequences that have deletions and/or additions, as well as those that have substitutions. As described below, the algorithms can account for gaps and the like. Typically, identity exists over a region comprising an antibody epitope, or a sequence that is at least about 25 amino acids or nucleotides in length, or over a region that is 50-100 amino acids or nucleotides in length, or over the entire length of the reference sequence.

The term “recombinant” when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all.

The term “heterologous” when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).

The term “antibody” refers to a polypeptide comprising a framework region from an immunoglobulin gene, or fragments thereof, that specifically bind and recognize an antigen, e.g., TIM3, a particular cell surface marker, or any desired target. Typically, the “variable region” contains the antigen-binding region of the antibody (or its functional equivalent) and is most critical in specificity and affinity of binding. See Paul, Fundamental Immunology (2003).

An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (V_(L)) and variable heavy chain (V_(H)) refer to these light and heavy chains respectively.

An “isotype” is a class of antibodies defined by the heavy chain constant region. Immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the isotype classes, IgG, IgM, IgA, IgD and IgE, respectively.

Antibodies can exist as intact immunoglobulins or as any of a number of well-characterized fragments that include specific antigen-binding activity. Such fragments can be produced by digestion with various peptidases. Pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)′₂, a dimer of Fab which itself is a light chain joined to V_(H)—C_(H)1 by a disulfide bond. The F(ab)′₂ may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab)′₂ dimer into an Fab′ monomer. The Fab′ monomer is essentially Fab with part of the hinge region (see Fundamental Immunology (Paul ed., 3d ed. 1993). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty et al., Nature 348:552-554 (1990)).

A “monoclonal antibody” refers to a clonal preparation of antibodies with a single binding specificity and affinity for a given epitope on an antigen. A “polyclonal antibody” refers to a preparation of antibodies that are raised against a single antigen, but with different binding specificities and affinities.

As used herein, “V-region” refers to an antibody variable region domain comprising the segments of Framework 1, CDR1, Framework 2, CDR2, and Framework 3, including CDR3 and Framework 4, which segments are added to the V-segment as a consequence of rearrangement of the heavy chain and light chain V-region genes during B-cell differentiation.

As used herein, “complementarity-determining region (CDR)” refers to the three hypervariable regions in each chain that interrupt the four “framework” regions established by the light and heavy chain variable regions. The CDRs are primarily responsible for binding to an epitope of an antigen. The CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3, numbered sequentially starting from the N-terminus, and are also typically identified by the chain in which the particular CDR is located. Thus, a V_(H) CDR3 is located in the variable domain of the heavy chain of the antibody in which it is found, whereas a V_(L) CDR1 is the CDR1 from the variable domain of the light chain of the antibody in which it is found.

The sequences of the framework regions of different light or heavy chains are relatively conserved within a species. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three dimensional space.

The amino acid sequences of the CDRs and framework regions can be determined using various well known definitions in the art, e.g., Kabat, Chothia, international ImMunoGeneTics database (IMGT), and AbM (see, e.g., Johnson et al., supra; Chothia & Lesk, (1987) J. Mol. Biol. 196, 901-917; Chothia et al. (1989) Nature 342, 877-883; Chothia et al. (1992) J. Mol. Biol. 227, 799-817; Al-Lazikani et al., J. Mol. Biol. 1997, 273(4)). Definitions of antigen combining sites are also described in the following: Ruiz et al. Nucleic Acids Res., 28, 219-221 (2000); and Lefranc Nucleic Acids Res. January 1; 29 (1):207-9 (2001); MacCallum et al., J. Mol. Biol., 262: 732-745 (1996); and Martin et al, Proc. Natl. Acad. Sci. USA, 86, 9268-9272 (1989); Martin, et al, Methods Enzymol., 203: 121-153, (1991); Pedersen et al, Immunomethods, 1, 126, (1992); and Rees et al, In Sternberg M. J. E. (ed.), Protein Structure Prediction. Oxford University Press, Oxford, 141-172 1996).

A “chimeric antibody” is an antibody molecule in which (a) the constant region, or a portion thereof, is altered, replaced or exchanged so that the antigen binding site (variable region, CDR, or portion thereof) is linked to a constant region of a different or altered class, effector function and/or species, or an entirely different molecule which confers new properties to the chimeric antibody (e.g., an enzyme, toxin, hormone, growth factor, drug, etc.); or (b) the variable region, or a portion thereof, is altered, replaced or exchanged with a variable region having a different or altered antigen specificity (e.g., CDR and framework regions from different species).

The antibody binds to an “epitope” on the antigen. The epitope is the specific antibody binding interaction site on the antigen, and can include a few amino acids or portions of a few amino acids, e.g., 5 or 6, or more, e.g., 20 or more amino acids, or portions of those amino acids. In some cases, the epitope includes non-protein components, e.g., from a carbohydrate, nucleic acid, or lipid. In some cases, the epitope is a three-dimensional moiety. Thus, for example, where the target is a protein, the epitope can be comprised of consecutive amino acids, or amino acids from different parts of the protein that are brought into proximity by protein folding (e.g., a discontinuous epitope). The same is true for other types of target molecules that form three-dimensional structures.

The term “specifically bind” refers to a molecule (e.g., antibody or antibody fragment) that binds to a target with at least 2-fold greater affinity than non-target compounds, e.g., at least 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 25-fold, 50-fold, or 100-fold greater affinity. For example, an antibody that specifically binds TIM3 will typically bind to TIM3 with at least a 2-fold greater affinity than a non-TIM3 target (e.g., a different TIM family member).

The term “binds” with respect to a cell type (e.g., an antibody that binds lymphoma cells), typically indicates that an agent binds a majority of the cells in a pure population of those cells. For example, an antibody that binds a given cell type typically binds to at least 2/3 of the cells in a population of the indicated cells (e.g., 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%). One of skill will recognize that some variability will arise depending on the method and/or threshold of determining binding.

The term “cross-linked” with respect to an antibody refers to attachment of the antibody to a solid or semisolid matrix (e.g., sepharose, beads, culture plate), or to another protein or antibody. For example, the antibody can be multimerized to create an antibody complex with multiple (more than 2) antigen-binding sites. The antibody can be multimerized by expressing the antibody as a high-valency isotype (e.g., IgA or IgM, which typically form complexes of 2 or 5 antibodies, respectively). Antibody multimerization can also be carried out by using a cross-linker comprising a reactive group capable of linking proteins (e.g., carbodiimide, NHS esters, etc). Methods and compositions for cross-linking an antibody to a matrix are described, e.g., in the Abcam and New England Biolab catalogs and websites (available at abcam.com and neb.com). Cross-linker compounds with various reactive groups are described, e.g., in Thermo Fisher Scientific catalog and website (available at piercenet.com).

As used herein, a first antibody, or an antigen-binding portion thereof, “competes” for binding to a target with a second antibody, or an antigen-binding portion thereof, when binding of the second antibody with the target is detectably decreased in the presence of the first antibody compared to the binding of the second antibody in the absence of the first antibody. The alternative, where the binding of the first antibody to the target is also detectably decreased in the presence of the second antibody, can, but need not be the case. That is, a second antibody can inhibit the binding of a first antibody to the target without that first antibody inhibiting the binding of the second antibody to the target. However, where each antibody detectably inhibits the binding of the other antibody to its cognate epitope or ligand, whether to the same, greater, or lesser extent, the antibodies are said to “cross-compete” with each other for binding of their respective epitope(s). Both competing and cross-competing antibodies are encompassed by the present invention. The term “competitor” antibody can be applied to the first or second antibody as can be determined by one of skill in the art. In some cases, the presence of the competitor antibody (e.g., the first antibody) reduces binding of the second antibody to the target by at least 10%, e.g., 20%, 30%, 40%, 50%, 60%, 70%, 80%, or more, e.g., so that binding of the second antibody to target is undetectable in the presence of the first (competitor) antibody.

The term “differentially expressed” or “differentially regulated” refers generally to a protein or nucleic acid biomarker that is overexpressed (upregulated) or underexpressed (downregulated) in one sample compared to at least one other sample. In the context of the present invention, the term generally refers to overexpression of a biomarker (TIM3) on a cancer cell compared to a normal, non-cancer cell.

For example, the terms “overexpressed” or “upregulated” interchangeably refer to a protein or nucleic acid, generally a biomarker, that is transcribed or translated at a detectably greater than control level. The term includes overexpression due to transcription, post transcriptional processing, translation, post-translational processing, cellular localization (e.g., organelle, cytoplasm, nucleus, cell surface), and RNA and protein stability. Overexpression can be detected using conventional techniques for detecting biomarkers, whether mRNA (i.e., RT-PCR, hybridization) or protein (i.e., flow cytometry, imaging, ELISA, immunohistochemical techniques). Overexpression can be 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more in comparison to a normal cell.

The terms “agonist,” “activator,” “inducer” and like terms refer to molecules that increase activity or expression as compared to a control. Agonists are agents that, e.g., bind to, stimulate, increase, activate, enhance activation, sensitize or upregulate the activity of the target. The expression or activity can be increased 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% 100% or more than that in a control. In certain instances, the activation is 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, or more in comparison to a control.

The terms “inhibitor,” “repressor” or “antagonist” or “downregulator” interchangeably refer to a substance that results in a detectably lower expression or activity level as compared to a control. The inhibited expression or activity can be 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or less than that in a control. In certain instances, the inhibition is 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, or more in comparison to a control.

A “control” sample or value refers to a sample that serves as a reference, usually a known reference, for comparison to a test sample. For example, a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control). A control can also represent an average value gathered from a number of tests or results. One of skill in the art will recognize that controls can be designed for assessment of any number of parameters. For example, a control can be devised to compare therapeutic benefit based on pharmacological data (e.g., half-life) or therapeutic measures (e.g., comparison of benefit and/or side effects). Controls can be designed for in vitro applications. One of skill in the art will understand which controls are valuable in a given situation and be able to analyze data based on comparisons to control values. Controls are also valuable for determining the significance of data. For example, if values for a given parameter are widely variant in controls, variation in test samples will not be considered as significant.

A “label” or a “detectable moiety” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include ³²P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins or other entities which can be made detectable, e.g., by incorporating a radiolabel into a peptide or antibody specifically reactive with a target peptide. Any method known in the art for conjugating an antibody to the label may be employed, e.g., using methods described in Hermanson, Bioconjugate Techniques 1996, Academic Press, Inc., San Diego.

A “labeled” molecule (e.g., nucleic acid, protein, or antibody) is one that is bound, either covalently, through a linker or a chemical bond, or noncovalently, through ionic, van der Waals, electrostatic, or hydrogen bonds to a label such that the presence of the molecule may be detected by detecting the presence of the label bound to the molecule.

The term “diagnosis” refers to a relative probability that a disorder such as cancer or an inflammatory condition is present in the subject. Similarly, the term “prognosis” refers to a relative probability that a certain future outcome may occur in the subject. For example, in the context of the present invention, prognosis can refer to the likelihood that an individual will develop cancer, have recurrence, or the likely severity of the disease (e.g., severity of symptoms, rate of functional decline, survival, etc.). The terms are not intended to be absolute, as will be appreciated by any one of skill in the field of medical diagnostics.

“Biopsy” or “biological sample from a patient” as used herein refers to a sample obtained from a patient having, or suspected of having, a TIM3 associated disorder. In some embodiments, the sample may be a tissue biopsy, such as needle biopsy, fine needle biopsy, surgical biopsy, etc. The sample can also be a blood sample or blood fraction, e.g., white blood cell fraction, serum, or plasma. The sample can comprise a tissue sample harboring a lesion or suspected lesion, although the biological sample may be also be derived from another site, e.g., a site of suspected metastasis, a lymph node, or from the blood. In some cases, the biological sample may also be from a region adjacent to the lesion or suspected lesion.

A “biological sample” can be obtained from a patient, e.g., a biopsy, from an animal, such as an animal model, or from cultured cells, e.g., a cell line or cells removed from a patient and grown in culture for observation. Biological samples include tissues and bodily fluids, e.g., blood, blood fractions, lymph, saliva, urine, feces, etc.

The terms “therapy,” “treatment,” and “amelioration” refer to any reduction in the severity of symptoms. In the case of treating cancer, treatment can refer to, e.g., reducing tumor size, number of cancer cells, growth rate, metastatic activity, reducing cell death of non-cancer cells, reduced nausea and other chemotherapy or radiotherapy side effects, etc. In the case of treating an inflammatory condition, the treatment can refer to, e.g., reducing blood levels of inflammatory cytokines, pain, swelling, recruitment of immune cells, etc. As used herein, the terms “treat” and “prevent” are not intended to be absolute terms. Treatment and prevention can refer to any delay in onset, amelioration of symptoms, improvement in patient survival, increase in survival time or rate, etc. Treatment and prevention can be complete (undetectable levels of neoplastic cells) or partial, such that fewer neoplastic cells are found in a patient than would have occurred without the present invention. The effect of treatment can be compared to an individual or pool of individuals not receiving the treatment, or to the same patient prior to treatment or at a different time during treatment. In some aspects, the severity of disease is reduced by at least 10%, as compared, e.g., to the individual before administration or to a control individual not undergoing treatment. In some aspects the severity of disease is reduced by at least 25%, 50%, 75%, 80%, or 90%, or in some cases, no longer detectable using standard diagnostic techniques.

The terms “effective amount,” “effective dose,” “therapeutically effective amount,” etc. refer to that amount of the therapeutic agent sufficient to ameliorate a disorder, as described above. For example, for the given parameter, a therapeutically effective amount will show an increase or decrease of therapeutic effect at least 5%, 10%, 15%, 20%, 25%, 40%, 50%, 60%, 75%, 80%, 90%, or at least 100%. Therapeutic efficacy can also be expressed as “-fold” increase or decrease. For example, a therapeutically effective amount can have at least a 1.2-fold, 1.5-fold, 2-fold, 5-fold, or more effect over a control.

As used herein, the term “pharmaceutically acceptable” is used synonymously with physiologically acceptable and pharmacologically acceptable. A pharmaceutical composition will generally comprise agents for buffering and preservation in storage, and can include buffers and carriers for appropriate delivery, depending on the route of administration.

The terms “dose” and “dosage” are used interchangeably herein. A dose refers to the amount of active ingredient given to an individual at each administration. For the present invention, the dose can refer to the concentration of the antibody or associated components, e.g., the amount of therapeutic agent or dosage of radiolabel. The dose will vary depending on a number of factors, including frequency of administration; size and tolerance of the individual; severity of the condition; risk of side effects; the route of administration; and the imaging modality of the detectable moiety (if present). One of skill in the art will recognize that the dose can be modified depending on the above factors or based on therapeutic progress. The term “dosage form” refers to the particular format of the pharmaceutical, and depends on the route of administration. For example, a dosage form can be in a liquid, e.g., a saline solution for injection.

“Subject,” “patient,” “individual” and like terms are used interchangeably and refer to, except where indicated, mammals such as humans and non-human primates, as well as rabbits, rats, mice, goats, pigs, and other mammalian species. The term does not necessarily indicate that the subject has been diagnosed with a particular disease, but typically refers to an individual under medical supervision. A patient can be an individual that is seeking treatment, monitoring, adjustment or modification of an existing therapeutic regimen, etc. A “cancer patient” can refer to an individual that has been diagnosed with cancer, is currently following a therapeutic regimen, or is at risk of recurrence, e.g., after surgery to remove a tumor. In some embodiments, the cancer patient has been diagnosed with cancer and is a candidate for therapy. Cancer patients can include individuals that have not received treatment, are currently receiving treatment, have had surgery, and those that have discontinued treatment.

In the context of treating cancer, a subject in need of treatment can refer to an individual that has cancer or a pre-cancerous condition, has had cancer and is at risk of recurrence, is suspected of having cancer, is undergoing standard treatment for cancer, such as radiotherapy or chemotherapy, etc. Similarly, in the context of treating inflammation, a subject in need to treatment can refer to an individual that has an inflammatory condition (e.g., an allergic or immune response), is at risk of developing inflammation from a preexisting condition (e.g., allergies), or is at risk of developing inflammation due to exposure or likely exposure to an inflammatory or antigenic substance, e.g., due to travel.

“Cancer”, “tumor,” “transformed” and like terms include precancerous, neoplastic, transformed, and cancerous cells, and can refer to a solid tumor, or a non-solid cancer (see, e.g., Edge et al. AJCC Cancer Staging Manual (7^(th) ed. 2009); Cibas and Ducatman Cytology: Diagnostic principles and clinical correlates (3^(rd) ed. 2009)). Cancer includes both benign and malignant neoplasms (abnormal growth). “Transformation” refers to spontaneous or induced phenotypic changes, e.g., immortalization of cells, morphological changes, aberrant cell growth, reduced contact inhibition and anchorage, and/or malignancy (see, Freshney, Culture of Animal Cells a Manual of Basic Technique (3^(rd) ed. 1994)). Although transformation can arise from infection with a transforming virus and incorporation of new genomic DNA, or uptake of exogenous DNA, it can also arise spontaneously or following exposure to a carcinogen.

The term “cancer” can refer to carcinomas, sarcomas, adenocarcinomas, lymphomas, leukemias, solid and lymphoid cancers, etc. Examples of different types of cancer include, but are not limited to, lung cancer (e.g., non-small cell lung cancer or NSCLC), ovarian cancer, prostate cancer, colorectal cancer, liver cancer (i.e., hepatocarcinoma), renal cancer (i.e., renal cell carcinoma), bladder cancer, breast cancer, thyroid cancer, pleural cancer, pancreatic cancer, uterine cancer, cervical cancer, testicular cancer, anal cancer, pancreatic cancer, bile duct cancer, gastrointestinal carcinoid tumors, esophageal cancer, gall bladder cancer, appendix cancer, small intestine cancer, stomach (gastric) cancer, cancer of the central nervous system, skin cancer, choriocarcinoma; head and neck cancer, blood cancer, osteogenic sarcoma, fibrosarcoma, neuroblastoma, glioma, melanoma, B-cell lymphoma, non-Hodgkin's lymphoma, Burkitt's lymphoma, Small Cell lymphoma, Large Cell lymphoma, monocytic leukemia, myelogenous leukemia, acute lymphocytic leukemia, acute myelocytic leukemia (AML), chronic myeloid leukemia (CML), and multiple myeloma. In some embodiments, the compositions and methods of the present invention are useful for treating cancer.

A “cancer target” or “cancer marker” is a molecule that is differentially expressed or processed in cancer, e.g., on a cancer cell or in the cancer milieu. Exemplary cancer targets are cell surface proteins such as TIM3 (also, e.g., cell adhesion molecules and receptors), intracellular receptors, hormones, and molecules such as proteases that are secreted by cells into the cancer milieu. Markers for specific cancers are known in the art, e.g., MUC1 expression on colon and colorectal cancers, bombesin receptors in lung cancer, and prostate specific membrane antigen (PSMA) on prostate cancer.

In some embodiments, the cancer target can be associated with a certain type of cancer cell, e.g., leukemia, myeloma, lymphoma, AML, non-small cell lung cancer cells, prostate cancer, colorectal cancer, breast cancer or ovarian cancer. A cell type specific target is typically expressed at levels at least 2 fold greater in that cell type than in a reference population of cells. In some embodiments, the cell type specific marker is present at levels at least 3, 4, 5, 6, 7, 8, 9, 10 20, 50, 100, or 1000 fold higher than its average expression in a reference population. Thus, the target can be detected or measured to distinguish the cell type or types of interest from other cells. For example, AML cancer targets include Ly86, LILRA1, and CD180.

A cancer stem cell (CSC) is a cell found in a tumor or blood cancer that can give rise to the cells that make up the bulk of the cancer. The CSC can also be self-renewing, similar to a normal (non-cancer) stem cell. CSCs can thus mediate metastasis by migrating to a non-tumor tissue in an individual and starting a “new” tumor. CSCs make up a very small percentage of any given cancer, depending on the stage that the cancer is detected. For example, the average frequency of CSCs in a sample of AML cells is believed to be about 1:10,000. Hematopoietic CSCs can be identified as CD34+, similar to normal hematopoietic stem cells (HSCs). Other CSC associated markers include CD44 (breast), CD133 (glial cancers), and Notch (e.g., myelomas and neuroblastoma).

An “inflammatory condition” refers to any inflammation in an individual, and can be transient (e.g., in response to exposure to a pathogen or allergen) or chronic. Inflammation is characterized by inflammatory cytokines such as IFN-gamma, IL-6, and TNF-alpha that recruit and activate macrophages and other leukocytes. In some cases, inflammation can develop into a chronic, harmful condition or autoimmune condition (e.g., MS, lupus, rheumatoid arthritis, Crohn's disease). Inflammation can be evident locally (e.g., at a localized site of infection or exposure) or systemically (e.g., atherosclerosis, high blood pressure).

II. TIM3 AND TIM3-ASSOCIATED DISORDERS

TIM3-associated disorders include cancers associated with elevated TIM3 expression and inflammatory disorders associated with reduced TIM3 expression, as described below. The antibodies of the invention can be used for diagnosis and monitoring of these disorders, as well as targeted therapy, e.g., in the case of delivering a chemotherapeutic (or cytotoxic) agent specifically to a TIM3-expressing cancer cell. In some cases, the targeted therapy can comprise contacting a TIM3-expressing cell with an antibody, as described herein.

TIM3 is expressed on Th1 (T helper type 1) cells, which are typically pro-inflammatory. As shown herein, however, TIM3 can be targeted as a negative regulator of pro-inflammatory pathways. Thus, some TIM3 specific antibodies described herein can be used in cases where it is desirable to reduce inflammation. TIM3 antibodies described herein can be used to reduce the onset or severity of autoimmune and inflammatory conditions, e.g., multiple sclerosis, rheumatoid arthritis, type I diabetes, Crohn disease, atherosclerosis, allergic conditions (e.g., allergic encephalomyelitis, asthma), and glomerulonephritis. Release of inflammatory cytokines (e.g., IFN-gamma) from activated T cells can lead to increased macrophage infiltration into an affected site, and increased tissue damage.

TIM3 is also associated with cancer cells and cancer stem cells, and binding TIM3 (e.g., with a TIM3 specific antibody, or a TIM3 specific antibody linked to a cytotoxic agent) can effectively inhibit cancer cell growth. The present TIM3 specific antibodies can also be used for diagnosis or localization of a TIM3 expressing cancer, optionally followed by targeted therapy using a TIM3 specific antibody (e.g., the same antibody, or a different TIM3 specific antibody with different binding characteristics).

The results described herein provide the first demonstration that TIM3 is expressed on B cell lymphoma cells. The presently described TIM3 specific antibodies can thus be used to target B cell lymphomas (e.g., for diagnostic and/or therapeutic applications) as well as the other cancers associated with TIM3 expression. TIM3 expression is associated with myelomas and other hematopoietic cell cancers, and carcinomas (e.g., carcinomas of the colon, ovary, liver, prostate, uterus, breast, and kidney). Examples of cancers that can be targeted using anti-TIM3 antibodies thus include hematopoietic cell cancers (e.g., B cell lymphoma, Burkitt's lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, myelodysplastic syndrome (preleukemia), leukemias, and myelomas (e.g., acute myeloid leukemia (AML), chronic myeloid leukemia (CML), chronic myelomoncytic leukemia (CMML), multiple myeloma, plasmacytoma)). Additional TIM3 expressing cancers that can be targeted using the presently disclosed antibodies include but are not limited to colon carcinoma, ovarian carcinoma, prostate carcinoma, breast carcinoma, renal carcinoma, liver carcinoma, and uterine carcinoma.

III. ANTI-TIM3 ANTIBODIES

Provided herein are anti-TIM3 antibodies (i.e., TIM3-specific antibodies, anti-TIM3) that specifically bind to the extracellular domain of TIM3. In some embodiments, the anti-TIM3 antibodies are rapidly internalized into TIM3-expressing cells (see, e.g., FIGS. 3 and 4). For example, in some embodiments, a higher percentage of the presently described TIM3 specific antibodies are internalized into TIM3-expressing cells than the 2E2 antibody at the same concentration, same temperature, and in the same time period (e.g., 1, 2, 5, 10, 20, or 30 minutes). In some embodiments, more than 30, 40, 50, 60, 70, 80% or higher percentage of the present TIM3 specific antibodies are internalized into a population of TIM3 expressing cells in less than 30 minutes. One of skill will appreciate that the amount of antibody and cell number will affect the percentage of antibody internalization. Typically, an excess of antibody is used (greater than 1 antibody/cell, e.g., at least 10³ antibody/cell) so that antibody concentration is not a limiting factor. The internalizing anti-TIM3 antibodies can thus be used to efficiently deliver a therapeutic agent to targeted TIM3-expressing cells (e.g. cancer cells).

Surprisingly, anti-TIM3 antibodies described herein can also inhibit growth of TIM3-expressing cells, when cross-linked or multimerized (see, e.g., FIG. 5). These anti-TIM3 antibodies can be used to inhibit cell growth of TIM3 expressing cells (e.g., cancer cells) in the absence of a conjugated cytotoxic agent.

Anti-TIM3 antibodies described herein also show complement dependent cytotoxicity (CDC) activity (see, e.g., FIG. 6). These anti-TIM3 antibodies can also thus be used to target TIM3 expressing cells for destruction, e.g. in the absence of a conjugated cytotoxic agent.

Also unexpected were anti-TIM3 antibodies described herein that can reduce release of inflammatory cytokines from activated T cells, and thereby reduce the severity of inflammatory responses (see, e.g., FIG. 7). Anti-TIM3 antibodies having this activity can thus be used to inhibit inflammation in individuals in need thereof.

Anti-TIM3 antibodies described herein have unique cell binding activities, for example, as described in Examples 2 and 3. For example, it was previously unknown that TIM3 could be used to target B cell lymphoma cells (exemplified as Pfeiffer cells). Yet the present results show that several of the disclosed anti-TIM3 antibodies are able to target these cells at a high level (see, e.g., FIGS. 3 and 4 and Table 2). In addition, several of the presently disclosed anti-TIM3 antibodies bind to leukemia cells, e.g., from AML patients, at a higher percentage and/or with high intensity than the 2E2 antibody (see, e.g., FIG. 2 and Tables 3 and 4). These antibodies can be used for detecting cancer cells that display an epitope that is targeted with high affinity by at least one of the anti-TIM3 antibodies disclosed herein. In some embodiments, those cancer cells can then be targeted for destruction with the same anti-TIM3 antibody. Such methods can include treating an individual having TIM3 expressing cancer cells, e.g., as described herein, comprising administering the anti-TIM3 antibody to the individual.

In some embodiments, the invention includes anti-TIM3 antibodies that compete for binding to TIM3 with a competitor antibody selected from the group consisting of:

-   -   an antibody having the CDR sequences of 1.7E10 (CDRH1-3=SEQ ID         NOs:3-5; CDRL1-3=SEQ ID NOs:8-10)     -   an antibody having the CDR sequences of 7.10F6 (CDRH1-3=SEQ ID         NOs:13-15; CDRL1-3=SEQ ID NOs:18-20);     -   an antibody having the CDR sequences of 8.16C10 (CDRH1-3=SEQ ID         NOs:23-25; CDRL1-3=SEQ ID NOs:28-30);     -   an antibody having the CDR sequences of 27.12E12 (CDRH1-3=SEQ ID         NOs:103-105; CDRL1-3=SEQ ID NOs:108-110);     -   an antibody having the CDR sequences of 27.2H4 (CDRH1-3=SEQ ID         NOs:33-35; CDRL1-3=SEQ ID NOs:38-40);     -   an antibody having the CDR sequences of 27.12A6 (CDRH1-3=SEQ ID         NOs:43-45; CDRL1-3=SEQ ID NOs:48-50);     -   an antibody having the CDR sequences of 9.1G12 (CDRH1-3=SEQ ID         NOs:113-115; CDRL1-3=SEQ ID NOs:118-120);     -   an antibody having the CDR sequences of 6.16F9 (CDRH1-3=SEQ ID         NOs:63-65; CDRL1-3=SEQ ID NOs:68-70);     -   an antibody having the CDR sequences of 6.14B9 (CDRH1-3=SEQ ID         NOs:53-55; CDRL1-3=SEQ ID NOs:58-60);     -   an antibody having the CDR sequences of 33.1G12 (CDRH1-3=SEQ ID         NOs:73-75; CDRL1-3=SEQ ID NOs:78-80);     -   an antibody having the CDR sequences of 33.2A5 (CDRH1-3=SEQ ID         NOs:83-85; CDRL1-3=SEQ ID NOs:88-90); and     -   an antibody having the CDR sequences of 33.14A5 (CDRH1-3=SEQ ID         NOs:93-95; CDRL1-3=SEQ ID NOs:98-100).

In some embodiments, the anti-TIM3 antibodies competes for binding with an antibody selected from the group consisting of:

-   -   an antibody comprising variable region sequences with         substantial identity (at least (85, 90, 95, or 98% identity) to         those of 1.7E10 (V1=SEQ ID NO:7; Vh=SEQ ID NO:2)     -   an antibody comprising variable region sequences with         substantial identity to those of 7.10F6 (V1=SEQ ID NO:17; Vh=SEQ         ID NO:12);     -   an antibody comprising variable region sequences with         substantial identity to those of 8.16C10 (V1=SEQ ID NO:27;         Vh=SEQ ID NO:22);     -   an antibody comprising variable region sequences with         substantial identity to those of 27.12E12 (V1=SEQ ID NO:107;         Vh=SEQ ID NO:102);     -   an antibody comprising variable region sequences with         substantial identity to those of 27.2H4 (V1=SEQ ID NO:37; Vh=SEQ         ID NO:32);     -   an antibody comprising variable region sequences with         substantial identity to those of 27.12A6 (V1=SEQ ID NO:47;         Vh=SEQ ID NO:42);     -   an antibody comprising variable region sequences with         substantial identity to those of 9.1G12 (V1=SEQ ID NO:117;         Vh=SEQ ID NO:112);     -   an antibody comprising variable region sequences with         substantial identity to those of 6.16F9 (V1=SEQ ID NO:67; Vh=SEQ         ID NO:62);     -   an antibody comprising variable region sequences with         substantial identity to those of 6.14B9 (V1=SEQ ID NO:57; Vh=SEQ         ID NO:52);     -   an antibody comprising variable region sequences with         substantial identity to those of 33.1G12 (V1=SEQ ID NO:77;         Vh=SEQ ID NO:72);     -   an antibody comprising variable region sequences with         substantial identity to those of 33.2A5 (V1=SEQ ID NO:87; Vh=SEQ         ID NO:82); and     -   an antibody comprising variable region sequences with         substantial identity to those of 33.14A5 (V1=SEQ ID NO:97;         Vh=SEQ ID NO:92).

Numerous types of competitive binding assays are known, including solid phase direct or indirect radioimmunoassay (RIA); solid phase direct or indirect enzyme immunoassay (EIA), sandwich competition assay (see Stahli et al., Methods in Enzymology 9:242-253 (1983)); solid phase direct biotin-avidin EIA (see Kirkland et al., J. Immunol. 137:3614-3619 (1986)); solid phase direct labeled assay; solid phase direct labeled sandwich assay (see Harlow and Lane, Antibodies, A Laboratory Manual, Cold Spring Harbor Press (1988)); solid phase direct label RIA using 1-125 label (see Morel et al., Molec. Immunol. 25(1):7-15 (1988)); solid phase direct biotin-avidin EIA (Cheung et al., Virology 176:546-552 (1990)); and direct labeled RIA (Moldenhauer et al., Scand. J. Immunol. 32:77-82 (1990)). Typically, such an assay involves the use of purified antigen bound to a solid surface or cells bearing either of these, an unlabelled test immunoglobulin and a labeled reference immunoglobulin. Competitive inhibition is measured by determining the amount of label bound to the solid surface or cells in the presence of the test immunoglobulin. Usually the test immunoglobulin is present in excess. Antibodies identified by competition assay (competing antibodies) include antibodies binding to the same epitope as the reference antibody and antibodies binding to an adjacent epitope sufficiently proximal to the epitope bound by the reference antibody for steric hindrance to occur. Usually, when a competing antibody is present in excess, it will inhibit specific binding of a reference antibody to a common antigen by at least 50 or 75%.

In some embodiments, the anti-TIM3 antibody binds the same epitope as an antibody selected from the group consisting of:

-   -   an antibody having the CDR sequences of 1.7E10 (CDRH1-3=SEQ ID         NOs:3-5; CDRL1-3=SEQ ID NOs:8-10)     -   an antibody having the CDR sequences of 7.10F6 (CDRH1-3=SEQ ID         NOs:13-15; CDRL1-3=SEQ ID NOs:18-20);     -   an antibody having the CDR sequences of 8.16C10 (CDRH1-3=SEQ ID         NOs:23-25; CDRL1-3=SEQ ID NOs:28-30);     -   an antibody having the CDR sequences of 27.12E12 (CDRH1-3=SEQ ID         NOs:103-105; CDRL1-3=SEQ ID NOs:108-110);     -   an antibody having the CDR sequences of 27.2H4 (CDRH1-3=SEQ ID         NOs:33-35; CDRL1-3=SEQ ID NOs:38-40);     -   an antibody having the CDR sequences of 27.12A6 (CDRH1-3=SEQ ID         NOs:43-45; CDRL1-3=SEQ ID NOs:48-50);     -   an antibody having the CDR sequences of 9.1G12 (CDRH1-3=SEQ ID         NOs:113-115; CDRL1-3=SEQ ID NOs:118-120);     -   an antibody having the CDR sequences of 6.16F9 (CDRH1-3=SEQ ID         NOs:63-65; CDRL1-3=SEQ ID NOs:68-70);     -   an antibody having the CDR sequences of 6.14B9 (CDRH1-3=SEQ ID         NOs:53-55; CDRL1-3=SEQ ID NOs:58-60);     -   an antibody having the CDR sequences of 33.1G12 (CDRH1-3=SEQ ID         NOs:73-75; CDRL1-3=SEQ ID NOs:78-80);     -   an antibody having the CDR sequences of 33.2A5 (CDRH1-3=SEQ ID         NOs:83-85; CDRL1-3=SEQ ID NOs:88-90); and     -   an antibody having the CDR sequences of 33.14A5 (CDRH1-3=SEQ ID         NOs:93-95; CDRL1-3=SEQ ID NOs:98-100).

In some embodiments, the anti-TIM3 antibody has light chain CDR sequences and heavy chain CDR sequences having up to 1, 2, or 3 amino acid substitutions, additions, or deletions/CDR relative to the CDR sequences of an antibody selected from the group consisting of 1.7E10, 7.10F6, 8.16C10, 22.12E12, 27.2H4, 9.1G12, 6.16F9, 6.14B9, 33.1G12, 33.2A5, and 33.14A5. In some embodiments, the light chain CDR sequences include up to 1, 2, or 3 amino acid substitutions, additions or deletions/CDR relative to the light chain CDR sequences of the aforementioned anti-TIM3 antibodies. In some embodiments, the heavy chain CDR sequences include up to 1, 2, or 3 amino acid substitutions, additions, or deletions/CDR relative to the heavy chain CDR sequences of the aforementioned anti-TIM3 antibodies. In some embodiments, substitution, addition or deletion occurs in only 1, 2, 3, 4, or 5 CDRs of the 6 total CDRs.

In some embodiments, the anti-TIM3 antibody is selected from the group consisting of:

-   -   an antibody having the CDR sequences of 1.7E10 (CDRH1-3=SEQ ID         NOs:3-5; CDRL1-3=SEQ ID NOs:8-10)     -   an antibody having the CDR sequences of 7.10F6 (CDRH1-3=SEQ ID         NOs:13-15; CDRL1-3=SEQ ID NOs:18-20);     -   an antibody having the CDR sequences of 8.16C10 (CDRH1-3=SEQ ID         NOs:23-25; CDRL1-3=SEQ ID NOs:28-30);     -   an antibody having the CDR sequences of 27.12E12 (CDRH1-3=SEQ ID         NOs:103-105; CDRL1-3=SEQ ID NOs:108-110);     -   an antibody having the CDR sequences of 27.2H4 (CDRH1-3=SEQ ID         NOs:33-35; CDRL1-3=SEQ ID NOs:38-40);     -   an antibody having the CDR sequences of 27.12A6 (CDRH1-3=SEQ ID         NOs:43-45; CDRL1-3=SEQ ID NOs:48-50);     -   an antibody having the CDR sequences of 9.1G12 (CDRH1-3=SEQ ID         NOs:113-115; CDRL1-3=SEQ ID NOs:118-120);     -   an antibody having the CDR sequences of 6.16F9 (CDRH1-3=SEQ ID         NOs:63-65; CDRL1-3=SEQ ID NOs:68-70);     -   an antibody having the CDR sequences of 6.14B9 (CDRH1-3=SEQ ID         NOs:53-55; CDRL1-3=SEQ ID NOs:58-60);     -   an antibody having the CDR sequences of 33.1G12 (CDRH1-3=SEQ ID         NOs:73-75; CDRL1-3=SEQ ID NOs:78-80);     -   an antibody having the CDR sequences of 33.2A5 (CDRH1-3=SEQ ID         NOs:83-85; CDRL1-3=SEQ ID NOs:88-90); and     -   an antibody having the CDR sequences of 33.14A5 (CDRH1-3=SEQ ID         NOs:93-95; CDRL1-3=SEQ ID NOs:98-100).

In some embodiments, the anti-TIM3 antibody is selected from the group consisting of:

-   -   an antibody having variable region sequences with at least 95%         identity to those of 1.7E10 (V1=SEQ ID NO:7; Vh=SEQ ID NO:2)     -   an antibody having variable region sequences with at least 95%         identity to those of 7.10F6 (V1=SEQ ID NO:17; Vh=SEQ ID NO:12);     -   an antibody having variable region sequences with at least 95%         identity to those of 8.16C10 (V1=SEQ ID NO:27; Vh=SEQ ID NO:22);     -   an antibody having variable region sequences with at least 95%         identity to those of 27.12E12 (V1=SEQ ID NO:107; Vh=SEQ ID         NO:102);     -   an antibody having variable region sequences with at least 95%         identity to those of 27.2H4 (V1=SEQ ID NO:37; Vh=SEQ ID NO:32);     -   an antibody having variable region sequences with at least 95%         identity to those of 27.12A6 (V1=SEQ ID NO:47; Vh=SEQ ID NO:42);     -   an antibody having variable region sequences with at least 95%         identity to those of 9.1G12 (V1=SEQ ID NO:117; Vh=SEQ ID         NO:112);     -   an antibody having variable region sequences with at least 95%         identity to those of 6.16F9 (V1=SEQ ID NO:67; Vh=SEQ ID NO:62);     -   an antibody having variable region sequences with at least 95%         identity to those of 6.14B9 (V1=SEQ ID NO:57; Vh=SEQ ID NO:52);     -   an antibody having variable region sequences with at least 95%         identity to those of 33.1G12 (V1=SEQ ID NO:77; Vh=SEQ ID NO:72);     -   an antibody having variable region sequences with at least 95%         identity to those of 33.2A5 (V1=SEQ ID NO:87; Vh=SEQ ID NO:82);         and     -   an antibody having variable region sequences with at least 95%         identity to those of 33.14A5 (V1=SEQ ID NO:97; Vh=SEQ ID NO:92).

In some embodiments, the antibody also has at least one activity selected from

-   -   Binding to TIM3 with a K_(D) of 100 nM or lower (e.g., 1-10 nM,         0.1-10 nM, 10-50 nM, about 20 nM, etc.);     -   Internalizing into TIM3-expressing cells at a higher rate than         the anti-TIM3 antibody 2E2;     -   Reducing release of IFN-gamma and/or IL-6 from activated CD4+ T         cells, compared to release in the absence of the antibody; and     -   Reducing cell growth of TIM3-expressing cells when cross-linked         or immobilized (e.g., on a solid or semisolid matrix), compared         to cell growth in the absence of the antibody.

Any of the antibodies described herein can be a chimeric antibody or a humanized antibody. In some embodiments, the antibody is a TIM3-binding antibody fragment, e.g., an Fab. In some embodiments, the anti-TIM3 antibody is labeled with a detectable agent, e.g., as described below. In some embodiments, the anti-TIM3 antibody is attached to a therapeutic agent, e.g., a chemotherapeutic or cytotoxic agent as described below.

In some embodiments, the anti-TIM3 antibody binds to TIM3 from a human. In some embodiments, the anti-TIM3 antibody binds to TIM3 from a rodent (mouse or rat).

A. Methods of Making Antibodies

For preparation of suitable antibodies of the invention and for use according to the invention, e.g., recombinant, monoclonal, or polyclonal antibodies, many techniques known in the art can be used (see, e.g., Kohler & Milstein, Nature 256:495-497 (1975); Kozbor et al., Immunology Today 4: 72 (1983); Cole et al., pp. 77-96 in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. (1985); Coligan, Current Protocols in Immunology (1991); Harlow & Lane, Antibodies, A Laboratory Manual (1988); and Goding, Monoclonal Antibodies: Principles and Practice (2d ed. 1986)). The genes encoding the heavy and light chains of an antibody of interest can be cloned from a cell, e.g., the genes encoding a monoclonal antibody can be cloned from a hybridoma and used to produce a recombinant monoclonal antibody. Gene libraries encoding heavy and light chains of monoclonal antibodies can also be made from hybridoma or plasma cells. Random combinations of the heavy and light chain gene products generate a large pool of antibodies with different antigenic specificity (see, e.g., Kuby, Immunology (3^(rd) ed. 1997)). Techniques for the production of single chain antibodies or recombinant antibodies (U.S. Pat. No. 4,946,778, U.S. Pat. No. 4,816,567) can be adapted to produce antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms such as other mammals, can be used to express humanized or human antibodies (see, e.g., U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, Marks et al., Bio/Technology 10:779-783 (1992); Lonberg et al., Nature 368:856-859 (1994); Morrison, Nature 368:812-13 (1994); Fishwild et al., Nature Biotechnology 14:845-51 (1996); Neuberger, Nature Biotechnology 14:826 (1996); and Lonberg & Huszar, Intern. Rev. Immunol. 13:65-93 (1995)). Alternatively, phage display technology can be used to identify antibodies and heteromeric Fab fragments that specifically bind to selected antigens (see, e.g., McCafferty et al., Nature 348:552-554 (1990); Marks et al., Biotechnology 10:779-783 (1992)). Antibodies can also be made bispecific, i.e., able to recognize two different antigens (see, e.g., WO 93/08829, Traunecker et al., EMBO J. 10:3655-3659 (1991); and Suresh et al., Methods in Enzymology 121:210 (1986)). Antibodies can also be heteroconjugates, e.g., two covalently joined antibodies, or immunotoxins (see, e.g., U.S. Pat. No. 4,676,980, WO 91/00360; WO 92/200373; and EP 03089).

Antibodies can be produced using any number of expression systems, including prokaryotic and eukaryotic expression systems. In some embodiments, the expression system is a mammalian cell expression, such as a hybridoma, or a CHO cell expression system. Many such systems are widely available from commercial suppliers. In embodiments in which an antibody comprises both a V_(H) and V_(L) region, the V_(H) and V_(L) regions may be expressed using a single vector, e.g., in a di-cistronic expression unit, or under the control of different promoters. In other embodiments, the V_(H) and V_(L) region may be expressed using separate vectors. A V_(H) or V_(L) region as described herein may optionally comprise a methionine at the N-terminus.

An antibody of the invention can also be produced in various formats, including as a Fab, a Fab′, a F(ab′)₂, a scFv, or a dAB. The antibody fragments can be obtained by a variety of methods, including, digestion of an intact antibody with an enzyme, such as pepsin (to generate (Fab′)₂ fragments) or papain (to generate Fab fragments); or de novo synthesis. Antibody fragments can also be synthesized using recombinant DNA methodology. In some embodiments, the anti-TIM3 antibody comprises F(ab′)₂ fragments that specifically bind TIM3. An antibody of the invention can also include a human constant region. See, e.g., Fundamental Immunology (Paul ed., 4d ed. 1999); Bird, et al., Science 242:423 (1988); and Huston, et al., Proc. Natl. Acad. Sci. USA 85:5879 (1988).

Methods for humanizing or primatizing non-human antibodies are also known in the art. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as import residues, which are typically taken from an import variable domain. Humanization can be essentially performed following the method of Winter and co-workers (see, e.g., Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al., Science 239:1534-1536 (1988) and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Such humanized antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.

In some cases, the antibody or antibody fragment can be conjugated to another molecule, e.g., polyethylene glycol (PEGylation) or serum albumin, to provide an extended half-life in vivo. Examples of PEGylation of antibody fragments are provided in Knight et al. Platelets 15:409, 2004 (for abciximab); Pedley et al., Br. J. Cancer 70:1126, 1994 (for an anti-CEA antibody); Chapman et al., Nature Biotech. 17:780, 1999; and Humphreys, et al., Protein Eng. Des. 20: 227, 2007). The antibody or antibody fragment can also be labeled, or conjugated to a therapeutic agent as described below.

B. Binding Affinity

The specificity of the binding can be defined in terms of the comparative dissociation constants (Kd) of the antibody (or other targeting moiety) for target, as compared to the dissociation constant with respect to the antibody and other materials in the environment or unrelated molecules in general. Typically, the Kd for the antibody with respect to the unrelated material will be at least 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 20-fold, 50-fold, 100-fold, 200-fold or higher than Kd with respect to the target.

The desired affinity for an antibody, e.g., high (pM to low nM), medium (low nM to 100 nM), or low (about 100 nM or higher), may differ depending upon whether it is being used as a diagnostic or therapeutic. Without being limited to theory, in one example, an antibody with medium affinity may be more successful in localizing to a tumor as compared to one with a high affinity. Thus, antibodies having different affinities can be used for diagnostic and therapeutic applications.

A targeting moiety will typically bind with a Kd of less than about 1000 nM, e.g., less than 250, 100, 50, 20 or lower nM. In some embodiments, the Kd of the affinity agent is less than 15, 10, 5, or 1 nM. In some embodiments, the Kd is 1-100 nM, 0.1-50 nM, 0.1-10 nM, or 1-20 nM. The value of the dissociation constant (Kd) can be determined by well-known methods, and can be computed even for complex mixtures by methods as disclosed, e.g., in Caceci et al., Byte (1984) 9:340-362.

Affinity of an antibody, or any targeting agent, for a target can be determined according to methods known in the art, e.g., as reviewed in Ernst et al. Determination of Equilibrium Dissociation Constants, Therapeutic Monoclonal Antibodies (Wiley & Sons ed. 2009).

Quantitative ELISA, and similar array-based affinity methods can be used. ELISA (Enzyme linked immunosorbent signaling assay) is an antibody-based method. In some cases, an antibody specific for target of interest is affixed to a substrate, and contacted with a sample suspected of containing the target. The surface is then washed to remove unbound substances. Target binding can be detected in a variety of ways, e.g., using a second step with a labeled antibody, direct labeling of the target, or labeling of the primary antibody with a label that is detectable upon antigen binding. In some cases, the antigen is affixed to the substrate (e.g., using a substrate with high affinity for proteins, or a Strepavidin-biotin interaction) and detected using a labeled antibody (or other targeting moiety). Several permutations of the original ELISA methods have been developed and are known in the art (see Lequin (2005) Clin. Chem. 51:2415-18 for a review).

The Kd, Kon, and Koff can also be determined using surface plasmon resonance (SPR), e.g., as measured by using a Biacore T100 system. SPR techniques are reviewed, e.g., in Hahnfeld et al. Determination of Kinetic Data Using SPR Biosensors, Molecular Diagnosis of Infectious Diseases (2004). In a typical SPR experiment, one interactant (target or targeting agent) is immobilized on an SPR-active, gold-coated glass slide in a flow cell, and a sample containing the other interactant is introduced to flow across the surface. When light of a given frequency is shined on the surface, the changes to the optical reflectivity of the gold indicate binding, and the kinetics of binding.

Binding affinity can also be determined by anchoring a biotinylated interactant to a streptaviden (SA) sensor chip. The other interactant is then contacted with the chip and detected, e.g., as described in Abdessamad et al. (2002) Nuc. Acids Res. 30:e45.

C. Internalization

TIM3-specific antibodies described herein can be internalized into TIM3-expressing cells, including TIM3-expressing lymphoma and AML cells. For example, TIM3 specific antibodies are shown in the Examples (and FIGS. 3 and 4) to be internalized into B lymphoma cells. In some cases, the disclosed antibodies are internalized at a higher rate, or at a higher level, than the 2E2 anti-TIM3 antibody. As demonstrated herein, the TIM3-specific antibodies described herein provide an effective means for targeting TIM3-expressing cells, e.g., with cytotoxic agents.

The percent internalization and internalization rate of an antibody can be evaluated by using methods known in the art, including, e.g., flow cytometry (FACS) and confocal fluorescent microscopy. Such methods are described, e.g., in Lue et al. (2007) Nature Protocols (Nature Med. 13:587-96); Cho et al. (2010) Biomacromolecules and Corbani et al. (2004) Endocrinology 145:2876-85, and as described herein.

For FACS and confocal microscopy, cells are incubated with a fluorescently-labeled targeting agent, e.g., antibody. The cells are typically selected to express the target of the labeled antibody, e.g., TIM3. Control cells can then be used that do not express the target. Internalization typically occurs at 37° C., but not at 4° C., which provides another control for the reaction. The cells can thus be contacted with the labeled agent and incubated at 37° C. or 4° C. (e.g., to detect binding without internalization).

Unbound, and surface-bound agent is removed by washing the cells, e.g., in an acid wash, followed by wash with a buffer at normal pH.

If adherent cells are used, the cells are removed from substrate prior to flow cytometry. The percentage of fluorescent cells indicates the percent internalization of the fluorescently-labeled agent. Percent internalization can also be expressed, e.g., as a percent of initial labeled agent added to the cells.

Internalization of an agent can also be evaluated by determining the localization of the fluorescently labeled agent by confocal microscopy. Methods of using confocal microscopy to determine internalization are described in, e.g., Xiao et al. (2008) Chem. Eur. J., 14:1769-1775. Briefly, the cells are contacted with labeled agent and incubated as described above. Following incubation, the cells can be incubated on ice, washed in PBS buffer at 4° C., treated with 0.25% trypsin (to remove from substrate, if applicable). The cell suspension can then be applied to slides for confocal fluorescent microscopy. Suitable confocal microscopes include the FV500-IX81 confocal microscope (Olympus America Inc.; Center Valley, Pa.) and Eclipse Ti-E (Nikon Instruments Inc.; Melville, N.Y.).

IV. DIAGNOSTIC APPLICATIONS

The antibodies described herein specifically bind TIM3 and TIM3-expressing cells. The TIM3-specific antibodies can thus be used for in vitro and in vivo diagnostic assays to detect TIM3-expressing cells (e.g., CSCs, certain solid tumor cells, and hematopoietic cancer cells as indicated herein). For example, a sample (e.g., blood sample or tissue biopsy) can be obtained from a patient and contacted with a TIM3 antibody, and the presence of a TIM3 expressing cell in the patient sample can be determined by detecting antibody binding. Antibody binding can be detected directly (e.g., where the antibody itself is labeled) or by using a second detection agent, such as a secondary antibody. The detectable label can be associated with an antibody of the invention, either directly, or indirectly, e.g., via a chelator or linker.

In some embodiments, the anti-TIM3 antibody is contacted with a biological sample from an individual having or suspected of having a TIM3 associated disorder, and antibody binding to a cell in the sample is determined, wherein higher or lower than normal antibody binding indicates that the individual has a TIM3 associated disorder. In some embodiments, the biological sample is a blood sample or blood fraction (e.g., serum, plasma, platelets, red blood cells, white blood cells). In some embodiments, the biological sample is a tissue sample (biopsy), e.g., from a suspected tumor site, or from a tissue that is known to be affected, e.g., to determine the boundaries of a known tumor. In some embodiments, the biological sample is obtained from a site of inflammation.

Biopsies are typically performed to obtain samples from tissues, i.e., non-fluid cell types. The biopsy technique applied will depend on the tissue type to be evaluated (e.g., breast, skin, colon, prostate, kidney, lung, bladder, lymph node, liver, bone marrow, airway or lung). In the case of a cancer the technique will also depend on the size and type of the tumor (e.g., solid, suspended, or blood), among other factors. Representative biopsy techniques include, but are not limited to, excisional biopsy, incisional biopsy, needle biopsy, surgical biopsy, and bone marrow biopsy. An “excisional biopsy” refers to the removal of an entire tumor mass with a small margin of normal tissue surrounding it. An “incisional biopsy” refers to the removal of a wedge of tissue that includes a cross-sectional diameter of the tumor. A diagnosis or prognosis made by endoscopy or fluoroscopy can require a “core-needle biopsy” of the tumor mass, or a “fine-needle aspiration biopsy” which generally obtains a suspension of cells from within the tumor mass. Biopsy techniques are discussed, for example, in Harrison's Principles of Internal Medicine, Kasper, et al., eds., 16th ed., 2005, Chapter 70, and throughout Part V.

Any method of detecting antibody binding to a cell in a sample can be used for the present diagnostic assays. Methods of detecting antibody binding are well known in the art, e.g., flow cytometry, fluorescent microscopy, ELISAs, etc. In some embodiments, the method comprises preparing the biological sample for detection prior to the determining step. For example, a subpopulation of cells (e.g., white blood cells) can be separated from the rest of the sample from the individual (e.g., other blood components) or cells in a tissue can be suspended for easier detection.

In some embodiments, the percentage of TIM3-expressing cells in the sample is determined and compared to a control, e.g., a sample from an individual or group of individuals that are known to have a TIM3 associated disorder (positive control) or from an individual or group of individuals that are known not to have a TIM3 associated disorder (normal, non-disease, or negative control). In some embodiments, the control is a standard range of TIM3 expression established for a given tissue. A higher or lower than normal percentage of TIM3 expressing cells, or higher or lower expression level, indicates that the individual has a TIM3 associated disorder.

In some embodiments, a labeled anti-TIM3 antibody can be provided (administered) to an individual to determine the applicability of an intended therapy. For example, a labeled antibody may be used to detect TIM3 density within a diseased area, where the density is typically high relative to non-diseased tissue. A labeled antibody can also indicate that the diseased area is accessible for therapy. Patients can thus be selected for therapy based on imaging results. Anatomical characterization, such as determining the precise boundaries of a cancer, can be accomplished using standard imaging techniques (e.g., CT scanning, MRI, PET scanning, etc.).

In some embodiments, labeled TIM3 specific antibodies as described herein can be further associated with a therapeutic compound, e.g., to form a “theranostic” composition. For example, an anti-TIM3 antibody described herein can be linked (directly or indirectly) to both a detectable label and a therapeutic agent, e.g., a cytotoxic agent to kill TIM3-expressing cancer cells. In some embodiments, a labeled TIM3 specific antibody is used for diagnosis and/or localization of a TIM3 expressing cancer cell, and the TIM3 expressing cancer cell is then targeted with a separate therapeutic TIM3 specific antibody. In some embodiments, the diagnostic TIM3 specific antibody is one that is not internalized into TIM3 expressing cells at a high rate or percentage. In some embodiments, the therapeutic TIM3 specific antibody is internalized into TIM3 expressing cells at a high rate or percentage (e.g., a higher rate than the 2E2 antibody, e.g., 1.7E10, 8.16C10, 27.2H4, 6.14B9), and is conjugated to a cytotoxic agent. In some embodiments, the therapeutic TIM3 specific antibody is an antibody that inhibits proliferation of TIM3 expressing cells upon crosslinking or multimerization (e.g., 1.7E10 or 7.10F6).

A. Labels

A diagnostic agent comprising an anti-TIM3 antibody can include any diagnostic agent known in the art, as provided, for example, in the following references: Armstrong et al., Diagnostic Imaging, 5^(th) Ed., Blackwell Publishing (2004); Torchilin, V. P., Ed., Targeted Delivery of Imaging Agents, CRC Press (1995); Vallabhajosula, S., Molecular Imaging: Radiopharmaceuticals for PET and SPECT, Springer (2009). A diagnostic agent can be detected by a variety of ways, including as an agent providing and/or enhancing a detectable signal. Detectable signals include, but are not limited to, gamma-emitting, radioactive, echogenic, optical, fluorescent, absorptive, magnetic, or tomography signals. Techniques for imaging the diagnostic agent can include, but are not limited to, single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), optical imaging, positron emission tomography (PET), computed tomography (CT), x-ray imaging, gamma ray imaging, and the like. The terms “detectable agent,” “detectable moiety,” “label,” “imaging agent,” and like terms are used synonymously herein.

In some embodiments, the label can include optical agents such as fluorescent agents, phosphorescent agents, chemiluminescent agents, and the like. Numerous agents (e.g., dyes, probes, labels, or indicators) are known in the art and can be used in the present invention. (See, e.g., Invitrogen, The Handbook—A Guide to Fluorescent Probes and Labeling Technologies, Tenth Edition (2005)). Fluorescent agents can include a variety of organic and/or inorganic small molecules or a variety of fluorescent proteins and derivatives thereof. For example, fluorescent agents can include but are not limited to cyanines, phthalocyanines, porphyrins, indocyanines, rhodamines, phenoxazines, phenylxanthenes, phenothiazines, phenoselenazines, fluoresceins, benzoporphyrins, squaraines, dipyrrolo pyrimidones, tetracenes, quinolines, pyrazines, corrins, croconiums, acridones, phenanthridines, rhodamines, acridines, anthraquinones, chalcogenopyrylium analogues, chlorins, naphthalocyanines, methine dyes, indolenium dyes, azo compounds, azulenes, azaazulenes, triphenyl methane dyes, indoles, benzoindoles, indocarbocyanines, benzoindocarbocyanines, and BODIPY™ derivatives. Fluorescent dyes are discussed, for example, in U.S. Pat. No. 4,452,720, U.S. Pat. No. 5,227,487, and U.S. Pat. No. 5,543,295.

The label can also be a radioisotope, e.g., radionuclides that emit gamma rays, positrons, beta and alpha particles, and X-rays. Suitable radionuclides include but are not limited to ²²⁵Ac, ⁷²As, ²¹¹At, ¹¹B, ¹²⁸Ba, ²¹²Bi, ⁷⁵Br, ¹⁴C, ¹⁰⁹Cd, ⁶²Cu, ⁶⁴Cu, ⁶⁷Cu, ¹⁸F, ⁶⁷Cu, ¹⁸F, ⁶⁷Ga, ⁶⁸Ga, ³H, ¹⁶⁶Ho, ¹²³I, ¹²⁴I, ¹²⁵I, ¹³⁰I, ¹³¹I, ¹¹¹I, ¹⁷⁷Lu, ¹³N, ¹⁵O, ³²P, ³³P, ²¹²Pb, ¹⁰³Pd, ¹⁸⁶Re, ¹⁸⁸Re, ⁴⁷Sc, ¹⁵³Sm, ⁸⁹Sr, ^(99m)Tc, ⁸⁸Y and ⁹⁰Y. In some embodiments, radioactive agents can include ¹¹¹In-DTPA, ^(99m)Tc(CO)₃-DTPA, ^(99m)Tc(CO)₃-ENPy2, ^(62/64/67)Cu-TETA, ^(99m)Tc(CO)₃-IDA, and ^(99m)Tc(CO)₃-triamines (cyclic or linear). In some embodiments, the agents can include DOTA and its various analogs with ¹¹¹In, ¹⁷⁷Lu, ¹⁵³Sm, ^(88/90)Y, ^(62/64/67)Cu, or ^(67/68)Ga. Ga. In some embodiments, a nanoparticle can be labeled by incorporation of lipids attached to chelates, such as DTPA-lipid, as provided in the following references: Phillips et al., Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 1 (1): 69-83 (2008); Torchilin, V. P. & Weissig, V., Eds. Liposomes 2nd Ed.: Oxford Univ. Press (2003); Elbayoumi, T. A. & Torchilin, V. P., Eur. J. Nucl. Med. Mol. Imaging. 33:1196-1205 (2006); Mougin-Degraef, M. et al., Intl J. Pharmaceutics 344:110-117 (2007).

In some embodiments, the diagnostic agent can be associated with a secondary binding ligand or to an enzyme (an enzyme tag) that will generate a colored product upon contact with a chromogenic substrate. Examples of suitable enzymes include urease, alkaline phosphatase, (horseradish) hydrogen peroxidase and glucose oxidase. Secondary binding ligands include, e.g., biotin and avidin or streptavidin compounds as known in the art.

In some embodiments, the labeled antibody can be further associated to a composition that improves stability in vivo, e.g. PEG or a nanoparticle such as a liposome, as described in more detail below.

B. Methods of Labeling

Techniques for conjugating detectable and therapeutic agents to antibodies are well known (see, e.g., Arnon et al., “Monoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapy”, in Monoclonal Antibodies And Cancer Therapy, Reisfeld et al. (eds.), pp. 243-56 (Alan R. Liss, Inc. 1985); Hellstrom et al., “Antibodies For Drug Delivery” in Controlled Drug Delivery (2nd Ed.), Robinson et al. (eds.), pp. 623-53 (Marcel Dekker, Inc. 1987); Thorpe, “Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review” in Monoclonal Antibodies '84: Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506 (1985); and Thorpe et al., “The Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates”, Immunol. Rev., 62:119-58 (1982)).

Typically, the antibody is attached to detectable moiety in an area that does not interfere with binding to the epitope. Thus in some cases, the detectable moiety is attached to the constant region, or outside the CDRs in the variable region. One of skill in the art will recognize that the optimal position for attachment may be located elsewhere on the antibody, so the position of the detectable moiety can be adjusted accordingly. In some embodiments, the ability of the antibody to associate with the epitope is compared before and after attachment to the detectable moiety to ensure that the attachment does not unduly disrupt binding.

In some embodiments, the antibody can be associated with an additional targeting moiety. For example, an antibody fragment, peptide, or aptamer that binds a different site on the target molecule or target cell can be conjugated to the antibody to optimize target binding, e.g., to a cancer cell.

V. THERAPEUTIC APPLICATIONS

TIM3 is aberrantly expressed in a number of disease states, and the TIM3-expressing cells in such conditions can be targeted using the TIM3-specific antibodies described herein. TIM3 expression is elevated on cancer cells (e.g., B cell lymphoma, AML cells, and solid tumor cells described herein) and CSCs (e.g., myeloid CSCs). TIM3 is not significantly expressed on normal hematopoietic stem cells (HSCs). A rapidly-internalized TIM3-targeted therapeutic antibody is particularly valuable in the case of myeloma, which has a very high rate of recurrence, though, as described herein, the present antibodies are useful for targeting and killing other TIM3-expressing cancers. As noted above, a therapeutic composition comprising an anti-TIM3 antibody can further include a detectable label to form a theranostic composition, e.g., for detection and localization of TIM3 expressing cells, and monitoring of therapeutic effect.

A. Chemotherapeutic and Cytotoxic Agents

As demonstrated herein, anti-TIM3 antibodies can inhibit cancer cell growth (proliferation), and thus can be considered chemotherapeutic agents. The following disclosure provides examples of chemotherapeutic and cytotoxic agents that can be linked to an anti-TIM3 antibody for delivery to TIM3-expressing cells.

A chemotherapeutic (anti-cancer) agent can be any agent capable of reducing cancer growth, interfering with cancer cell replication, directly or indirectly killing cancer cells, reducing metastasis, reducing tumor blood supply, etc. Chemotherapeutic agents thus include cytotoxic agents. Cytotoxic agents include but are not limited to saporin, taxanes, vinca alkaloids, anthracycline, and platinum-based agents. Classes of chemotherapeutic agents include but are not limited to alkylating agents, antimetabolites, e.g, methotrexate, plant alkaloids, e.g., vincristine, and antibiotics, e.g., doxorubicin as well as miscellaneous drugs that do not fall in to a particular class such as hydroxyurea. Platinum-based drugs, exemplified by cisplatin and oxaliplatin, represent a major class of chemotherapeutics. These drugs bind to DNA and interfere with replication. Taxanes, exemplified by taxol, represent another major class of chemotherapeutics. These compounds act by interfering with cytoskeletal and spindle formation to inhibit cell division, and thereby prevent growth of rapidly dividing cancer cells. Other chemotherapeutic drugs include hormonal therapy.

Chemotherapeutics currently used for treating myeloma include bortezomib, lenalidomide, and thalidomide. Additional therapeutic agents that can be administered to myeloma patients include bisphosphonates (to prevent bone fractures) and erythropoietin (to reduce anemia).

More than one therapeutic agent can be combined, either in the same composition, or in separate compositions. The therapeutic agent(s) can also be combined with additional therapeutic agents as appropriate for the particular individual. Common therapeutic agents provided to cancer patients include medications to address pain, nausea, anemia, infection, inflammation, and other symptoms commonly experienced by cancer patients.

B. Methods of Forming Therapeutic Compositions

Antibodies can be attached to a therapeutic agent, detectable agent, or nanocarrier using a variety of known cross-linking agents. Methods for covalent or non-covalent attachment of polypeptides are well known in the art. Such methods may include, but are not limited to, use of chemical cross-linkers, photoactivated cross-linkers and/or bifunctional cross-linking reagents. Exemplary methods for cross-linking molecules are disclosed in U.S. Pat. No. 5,603,872 and U.S. Pat. No. 5,401,511. Non-limiting examples of cross-linking reagents include glutaraldehyde, bifunctional oxirane, ethylene glycol diglycidyl ether, carbodiimides such as 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide or dicyclohexylcarbodiimide, bisimidates, dinitrobenzene, N-hydroxysuccinimide ester of suberic acid, disuccinimidyl tartarate, dimethyl-3,3′-dithio-bispropionimidate, azidoglyoxal, N-succinimidyl-3-(2-pyridyldithio)propionate and 4-(bromoadminoethyl)-2-nitrophenylazide.

For antibodies conjugated to nanocarriers (e.g., liposomes), a certain number of antibodies will be present on the surface, i.e., at a given surface density. In some embodiments, the nanocarrier will have at least 5 antibodies per nanocarrier, e.g., at least 10, 30, 40, 50, 75, 100 or higher antibodies per nanocarrier. One of skill in the art will understand that surface density represents an average range, as the number of antibodies per nanocarrier will not be absolutely uniform for all members of the population.

Nanocarriers include vesicles such as liposomes and micelles, as well as polymeric nanoparticles, etc. Nanocarriers are useful for delivery of therapeutic and diagnostic agents, but can be particularly useful for shielding cytotoxic agents used to treat cancer. The nanocarrier can comprise lipids (e.g., phospholipids), hydrophilic polymers, hydrophobic polymers, amphipatic compounds, cross-linked polymers, and a polymeric matrix (see, e.g., WO2009/110939). Depending on the application, the nanocarrier can be designed to have a particular size, half-life, shelf life, and leakage rate.

Preparation of nanocarriers, such as an antibody targeted liposome, polymeric nanoparticle, or extended shelf-life liposome, is described, e.g., in U.S. Pat. Nos. 6,465,188, 7,122,202, 7,462,603 and 7,550,441.

In some embodiments, the antibody is linked to a stabilizing moiety such as PEG, or a liposome or other nanocarrier. U.S. Pat. Nos. 4,732,863 and 7,892,554 and Chattopadhyay et al. (2010) Mol Pharm 7:2194 describe methods for attaching the selected antibody to PEG, PEG derivatives, and nanoparticles (e.g., liposomes). Liposomes containing phosphatidyl-ethanolamine (PE) can be prepared by established procedures as described herein. The inclusion of PE provides an active functional site on the liposomal surface for attachment.

The antibody conjugate can also be formulated to provide more than one active compound, e.g., additional chemotherapeutic or cytotoxic agents, cytokines, or growth inhibitory agents. The active ingredients may also prepared as sustained-release preparations (e.g., semi-permeable matrices of solid hydrophobic polymers (e.g., polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides. The antibodies and immunocongugates can be entrapped in a nanoparticle prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions.

VI. METHODS OF ADMINISTRATION

The anti-TIM3 antibodies of the invention can efficiently deliver a therapeutic composition to TIM3-expressing cells in vivo. In some embodiments, the method of treatment comprises administering to an individual an effective amount of a therapeutic anti-TIM3 conjugate, e.g., an anti-TIM3 antibody attached to a therapeutic agent. In some embodiments, the individual has been diagnosed with cancer. In some embodiments, the individual is receiving or has received cancer therapy, e.g., surgery, radiotherapy, or chemotherapy. In some embodiments, the individual has been diagnosed, but the cancer is in remission.

In some embodiments, the anti-TIM3 conjugate includes a liposome. In some embodiments, the method further comprises monitoring the individual for progression of the cancer. In some embodiments, the dose of the anti-TIM3 conjugate for each administration is determined based on the therapeutic progress of the individual, e.g., where a higher dose of chemotherapeutic is administered if the individual is not responding sufficiently to therapy.

In some embodiments, the invention can include an antibody or antibody-targeted composition and a physiologically (i.e., pharmaceutically) acceptable carrier. The term “carrier” refers to a typically inert substance used as a diluent or vehicle for a diagnostic or therapeutic agent. The term also encompasses a typically inert substance that imparts cohesive qualities to the composition. Physiologically acceptable carriers can be liquid, e.g., physiological saline, phosphate buffer, normal buffered saline (135-150 mM NaCl), water, buffered water, 0.4% saline, 0.3% glycine, glycoproteins to provide enhanced stability (e.g., albumin, lipoprotein, globulin, etc.), and the like. Since physiologically acceptable carriers are determined in part by the particular composition being administered as well as by the particular method used to administer the composition, there are a wide variety of suitable formulations of pharmaceutical compositions of the present invention (See, e.g., Remington's Pharmaceutical Sciences, 17^(th) ed., 1989).

The compositions of the present invention may be sterilized by conventional, well-known sterilization techniques or may be produced under sterile conditions. Aqueous solutions can be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration. The compositions can contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents, and the like, e.g., sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, and triethanolamine oleate. Sugars can also be included for stabilizing the compositions, such as a stabilizer for lyophilized antibody compositions.

Dosage forms can be prepared for mucosal (e.g., nasal, sublingual, vaginal, buccal, or rectal), parenteral (e.g., subcutaneous, intravenous, intramuscular, or intraarterial injection, either bolus or infusion), oral, or transdermal administration to a patient. Examples of dosage forms include, but are not limited to: dispersions; suppositories; ointments; cataplasms (poultices); pastes; powders; dressings; creams; plasters; solutions; patches; aerosols (e.g., nasal sprays or inhalers); gels; liquid dosage forms suitable for oral or mucosal administration to a patient, including suspensions (e.g., aqueous or non-aqueous liquid suspensions, oil-in-water emulsions, or a water-in-oil liquid emulsions), solutions, and elixirs; liquid dosage forms suitable for parenteral administration to a patient; and sterile solids (e.g., crystalline or amorphous solids) that can be reconstituted to provide liquid dosage forms suitable for parenteral administration to a patient.

Injectable (e.g., intravenous) compositions can comprise a solution of the antibody or antibody-targeted composition suspended in an acceptable carrier, such as an aqueous carrier. Any of a variety of aqueous carriers can be used, e.g., water, buffered water, 0.4% saline, 0.9% isotonic saline, 0.3% glycine, 5% dextrose, and the like, and may include glycoproteins for enhanced stability, such as albumin, lipoprotein, globulin, etc. Often, normal buffered saline (135-150 mM NaCl) will be used. The compositions can contain pharmaceutically acceptable auxiliary substances to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents, e.g., sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc. In some embodiments, the antibody-targeted composition can be formulated in a kit for intravenous administration.

Formulations suitable for parenteral administration, such as, for example, by intraarticular (in the joints), intravenous, intramuscular, intratumoral, intradermal, intraperitoneal, and subcutaneous routes, include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. Injection solutions and suspensions can also be prepared from sterile powders, granules, and tablets. In the practice of the present invention, compositions can be administered, for example, by intravenous infusion, topically, intraperitoneally, intravesically, or intrathecally. Parenteral administration and intravenous administration are the preferred methods of administration. The formulations of targeted compositions can be presented in unit-dose or multi-dose sealed containers, such as ampoules and vials.

The targeted delivery composition of choice, alone or in combination with other suitable components, can be made into aerosol formulations (“nebulized”) to be administered via inhalation. Aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, and nitrogen.

The pharmaceutical preparation can be packaged or prepared in unit dosage form. In such form, the preparation is subdivided into unit doses containing appropriate quantities of the active component, e.g., according to the dose of the therapeutic agent or concentration of antibody. The unit dosage form can be a packaged preparation, the package containing discrete quantities of preparation. The composition can, if desired, also contain other compatible therapeutic agents.

The antibody (or antibody-targeted composition) can be administered by injection or infusion through any suitable route including but not limited to intravenous, subcutaneous, intramuscular or intraperitoneal routes. An example of administration of a pharmaceutical composition includes storing the antibody at 10 mg/ml in sterile isotonic aqueous saline solution for injection at 4° C., and diluting it in either 100 ml or 200 ml 0.9% sodium chloride for injection prior to administration to the patient. The antibody is administered by intravenous infusion over the course of 1 hour at a dose of between 0.2 and 10 mg/kg. In other embodiments, the antibody is administered by intravenous infusion over a period of between 15 minutes and 2 hours. In still other embodiments, the administration procedure is via sub-cutaneous bolus injection.

The dose of antibody is chosen in order to provide effective therapy for the patient and is in the range of less than 0.1 mg/kg body weight to about 25 mg/kg body weight or in the range 1 mg-2 g per patient. In some cases, the dose is in the range 1-100 mg/kg, or approximately 50 mg-8000 mg/patient. The dose may be repeated at an appropriate frequency which may be in the range once per day to once every three months, depending on the pharmacokinetics of the antibody (e.g., half-life of the antibody in the circulation) and the pharmacodynamic response (e.g., the duration of the therapeutic effect of the antibody). In some embodiments, the in vivo half-life of between about 7 and about 25 days and antibody dosing is repeated between once per week and once every 3 months.

Administration can be periodic. Depending on the route of administration, the dose can be administered, e.g., once every 1, 3, 5, 7, 10, 14, 21, or 28 days or longer (e.g., once every 2, 3, 4, or 6 months). In some cases, administration is more frequent, e.g., 2 or 3 times per day. The patient can be monitored to adjust the dosage and frequency of administration depending on therapeutic progress and any adverse side effects, as will be recognized by one of skill in the art.

Thus in some embodiments, additional administration is dependent on patient progress, e.g., the patient is monitored between administrations. For example, after the first administration or round of administrations, the patient can be monitored for rate of tumor growth, recurrence (e.g., in the case of a post-surgical patient), or general disease-related symptoms such as weakness, pain, nausea, etc.

In therapeutic use for the treatment of cancer, an antibody-targeted composition (e.g., including a therapeutic and/or diagnostic agent) can be administered at the initial dosage of about 0.001 mg/kg to about 1000 mg/kg daily and adjusted over time. A daily dose range of about 0.01 mg/kg to about 500 mg/kg, or about 0.1 mg/kg to about 200 mg/kg, or about 1 mg/kg to about 100 mg/kg, or about 10 mg/kg to about 50 mg/kg, can be used. The dosage is varied depending upon the requirements of the patient, the severity of the condition being treated, and the targeted composition being employed. For example, dosages can be empirically determined considering the type and stage of cancer diagnosed in a particular patient. The dose administered to a patient, in the context of the present invention, should be sufficient to affect a beneficial therapeutic response in the patient over time. The size of the dose will also be determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a particular targeted composition in a particular patient, as will be recognized by the skilled practitioner.

It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entireties for all purposes.

VII. EXAMPLES A. Example 1 TIM3-Specific Antibodies

Female Balb/C mice were immunized with recombinant human TIM3-Fc fusion protein four times. Two days after final injection, spleen and lymph node cells were fused with SP2/O cells using PEG and selected in HAT medium. Hybridomas were screened by ELISA for reactivity against recombinant TIM3 protein and positive cultures were confirmed by flow cytometry for recognition of TIM3 expressing cell lines. Selected hybridoma were subcloned by limiting dilution or single cell sorting. Subclones were confirmed by flow cytometry for binding to TIM3. Heavy chain and light chain variable region sequences were amplified using reverse transcriptase polymerase chain reaction (RT-PCR) with specific primers. cDNA products were then sequenced. Table 1 (SEQ ID NOS:3-5, 8-10; 13-15, 18-20; 23-25, 28-30; 73-75, 78-80; 83-85, 88-90; 93-95, 98-100; 103-105, 108-110; 33-35, 38-40; 43-45, 48-50; 53-55, 58-60; 63-65, 68-70; 113-115, 118-120) profiles the selected antibodies, e.g., for isotype and CDR sequences.

TABLE 1 Hybridoma Isotype VH DH JH VK JK 1.7E 10 IgG1, k IGHV4- DSP.9 JH4 IGKV3- JK2 1*02 5*01 7.10F6 IgG1, k IGHV5- DSP2.10 JH4 IGKV8- JK2 6-3*01 27*01 8.16C10 IgG1, k IGHV1- DSP2.4 JH4 IGKV4- JK2 11*02 79*01 33.1G12 IgG1, k IGHV1- DSP2.2 JH4 IGKV3- JK1 20*02 5*01 33.2A5 IgG1, k VHJ558 IGHD2-14*01 JH4 IGKV3- JK2 4*01 33.14A5 IgG1, k J558.46 DSP2.8 JH3 Igk- JK5 V4/5 27.12 E12 IgG2b, k IGHV14- DFL16.2 JH1 IGKV6- JK2 1*02 15*01 27.2H4 IgG1, k IGHV14- DST4.3 JH4 IGKV6- JK1 1*02 17*01 27.12A6 IgG1, k IGHV5- DSP2.8 JH4 IGKV8- JK1 12-2*01 27*01 6.14B9 IgG1, k IGHV3- DSP2.6 JH2 IGKV9-  JK5 2*03 124*01 6.16F9 IgG1, k IGHV5- DSP2.8 JH4 IGKV8- JK1 12-2*01 27*01 9.1G12 IgG2b, 1 IGHV5S9*01, DSP2.12 JH3 Jk5 Hybridoma CDRH1 CDRH2 CDRH3 CDRL1 CDRL2 CDRL3 1.7E 10 GFDFSRYW INPDSSTI ARPSYDGYYGYAMDY ESVDSYGKSF RAS QQSNEDPYT 7.10F6 GFIFSGYG INSNGGSV ARIYYRCMDY QSLLYSSNQKNY WAS HQYLSSYT 8.16C10 GYTFTDYY IYPGSGIT AIYGYDGGYAMDY SSVSSNY STS HQWSTYPYT 33.1G12 GYSFTGYL INPYNGDI ARRDENFDYDNAMDY ESVDIYGNSF RAS QQSNEDPWT 33.2A5 GYTSNYNW INPATGYT TTGRNDEGGYALDS QSVDHAGDSY GAS QQSNEDPYT 33.14A5 GYTFTSYW. IDPSKSET AQYGNHVLLLTGAKGHRSLSLH SSVSSNY STS QLYSGYPLT 27.12 E12 GFNIKDYY IDPENVKT TRDFGYVGFFDV QNVGTN SAS QQYNSYPLT 27.2H4 GFNIKHYY IDPETGNT ARGWSYAMDY QDVNTA SAS QQHYSTPWT 27.12A6 GFTFSSYT ISSGGHST ARGGYGNYGPYYNMDY QSVLYSSNQKNY WAS HQYLSSWT 6.14B9 GYSITSDYA ISYSGSI ARSGRLRRDFDY QEISGY AAS LQYASYPLT 6.16F9 GFTFSSYT TSSSGAST ARGGYGNYGPYYALDY QSVLYSSNQKNY WAS HQYLSSWT 9.1G12 GFTFSSYA ISSGGTYT VRPDYTHDDGGFAY QGISNN DAS LQHRYLPHVRCW

The polynucleotide and protein sequences for the heavy and light chain variable regions are provided in the sequence listing.

B. Example 2 Binding Profile for TIM3-Specific Antibodies

The binding profile of the selected TIM3-specific antibodies was tested on various TIM3-expressing cell lines. Table 2 shows the percentage of cell binding of the indicated antibodies to Pfeiffer cells, Daudi cells, and CMK cells. TIM3 2E2 is an antibody commercially available from eBioscience®, San Diego, Calif. (see, e.g., the website and catalog available at ebioscience.com, catalog number 17-3109, Hastings et al. (2009) Eur. J. Immunol. 39:2492).

TABLE 2 Profile of Tim3-specific antibody binding to myeloid and lymphoma cell lines FACS staining (Percent binding) Cell Line Disease 1.7E10 7.10F6.1 8.16C10 9.1G12 27.2H4 27.12E12 Tim3 2E2 Pfeiffer Non 97% 92% 85% 14% 75% 97% 97% Hodgkin's (Geomean = (Geomean = (Geomean = Lymphoma. 439) 458) 308) Diffuse large 91% B cell Lymphoma Daudi Burkitt's 95% 98% 67% Neg. 46% 92% 90% Lymphoma 97% CMK Acute 32% ND ND  2% Neg. 18% 19% megakaryo- cytic leukemia. AML-M7

The TIM3-specific antibodies were also tested for binding to peripheral blood cells from a normal (non-cancer) donor. As shown for 1.7E10 in FIG. 1, the antibodies do not bind significantly to mature peripheral blood cells, with the exception of low level binding to a small population of monocytes.

C. Example 3 Binding of TIM3-Specific Antibodies to Cancer Patient Samples

In contrast to the lack of binding to normal peripheral blood cells, the Tim3-specific antibodies bind at a high level to AML cells from patient samples. FIG. 2 compares the peripheral blood binding profiles of Isotype control (msIgG1) and 2E2 antibodies to those for the 1.7E10, 7.10F6, and 8.16C10 antibodies. The 1.7E10.7 and 7.10F6 bind to significantly more cells, with higher fluorescence, than the commercially available antibody. The 8.16C10 antibody binds about the same number of cells as 2E2 at a slightly higher fluorescence.

Table 3 shows the binding profiles for peripheral blood from five different AML patient samples. In this case, the peripheral blood was separated into stem cell (CD34+CD38−) and blast cells. Table 4 shows the binding profiles for these populations obtained from bone marrow.

TABLE 3 Percent binding of TIM3-specific antibodies to PBMCs from AML patients ID Population Diagnosis 1.7E10 7.10F6 8.16C10 27.12E12 27.2H4 9.1G12 TIM3 2E2 1 Blast AML with 18.31%  13.49% 3.13% N/A N/A N/A  2.92% CD34+CD38− myelodysplasia- 25.34%  18.70% 4.67% N/A N/A N/A  3.26% related change 2 Blast AML with 0.24% 78.74% 68.09%  N/A N/A N/A 59.34% CD34+CD38− myelodysplasia- 0.19% 85.78% 76.43%  N/A N/A N/A 64.78% related change 3 Blast unknown 3.89%  1.33% 0.83% 27.86% 1.07% 0.67%  1.01% CD34+CD38− 1.00%  0.60% 0.49%  2.66% 0.69% 0.23%  0.17% 4 Blast AML with   88%   94%   78% NA NA NA NA CD34+CD38− monocytic   94%   98%   87% NA differentiation 5 Blast Persistent/   29%   49%   25% NA NA NA NA CD34+CD38− recurrent AML   29%   49%   25% NA (MDS/MPD)

TABLE 4 Percent binding of Tim3-specific antibodies to bone marrow cells from AML patients ID Population Diagnosis 1.7E10 7.10F6 8.16C10 27.12E12 27.2H4 9.1G12 Tim3 2E2 1 Blast Persistent/ 34.79%  18.96%  55.59% NA NA NA NA CD34+CD38− recurrent AML  5.8% 8.61% 19.19% NA NA NA 2 Blast AML with 1.52% 8.37%  2.61% NA NA NA 1.80% CD34+CD38− t(8; 21)(q22; q22) 0.60% 4.83%  1.47% NA NA NA  1.6%

D. Example 4 Internalization of TIM3-Specific Antibodies

The TIM3-specific antibodies were tested for internalization into TIM3-expressing cells (Pfeiffer B lymphoma cells). Pfeiffer cells were blocked with ice-cold PBS+3% human serum, followed by pre-incubation for 20 minutes at 4C with the TIM3-specific antibodies or their corresponding isotype controls. Most of the TIM3-specific antibodies disclosed here are IgG1, though 27.12E12 is IgG2b. The cells were washed 3× with PBS and split into two sets for 20 minute incubations. The first set was incubated at 4C, where internalization occurs at a very low level if at all, while the second set was incubated at 37C. After incubation, the cells were washed with PBS and incubated with goat anti-mouse PE.

FIG. 3 shows the results, expressed as a ratio of cell surface staining at 37C/cell surface staining at 4C. Thus, the more internalization, the lower the ratio. From the results shown in FIG. 3, the 1.7E10, 8.16C10, 9.1G12, 27.2H4, 24.6C9.10, and 6.14B9 antibodies show significant levels of internalization. In particular, more than 50% of the 1.7E10, 8.16C10, 27.2H4, and 6.14B9 antibodies are internalized after 20 minutes.

E. Example 5 Use of TIM3-Specific Antibodies for Antibody Drug Conjugates (ADC)

Given the internalization results, the TIM3-specific antibodies were also tested for ability to kill TIM3-expressing cells when conjugated to a cytotoxic drug. The TIM3-specific antibodies were affinity purified using a Protein G column. The purified antibodies were biotinylated using EZ-link Sulfo NHS-LC-Biotinylated kit (ThermoFisher Scientific). Strepavidin-saporin conjugates (SAv-ZAP) were purchased from Advanced Targeting Systems. Saporin is a potent Type I ribosome inactivating toxin. SAv-ZAP was conjugated to the biotinylated antibodies at room temperature for 45 minutes. Pfeiffer cells were treated with different TIM3-specific antibodies or isotype controls at 5 nM for 72 hours. After 72 hours, cell viability was measured using the DHL™ Cell Cytotoxicity Assay kit. The assay measures released cytoplasmic lactate dehydrogenase (LDH) to determine cell membrane integrity and quantify cytotoxicity.

FIG. 4 shows the cytotoxicity results. The antibody-saporin conjugates (ADCs) are designated BZAP. Data are shown are presented as the mean of triplicates with bars showing standard deviation.

The data show that the TIM3-specific antibodies are capable of ADC activity. Of particular interest is the high level of cytotoxicity shown by the 27.12E12-BZAP and 9.1G12-BZAP antibody conjugates, which are of the IgG2 isotype.

Table 5 provides an overview of the data that indicates the level of TIM3 binding and binding profile for the antibodies and antibody conjugates.

TABLE 5 TIM3 binding profiles of antibody conjugates GeoMean Anti-TIM3 (Intensity of antibody IDs TIM3 binding) % Positive for TIM3 Mouse IgG1k-Biotin 5.06 0.192 mouse 2E2-pure 198 89.9 1.7E10.12-Biotin 354 99.2 7.10F6.1-pure 142 93.3 8.16C10.18-pure 83.8 92.5 6.14B9-Biotin 20.4 48.2 Mouse IgG1k-BZAP 5.33 0.501 1.7E10.12-BZAP 436 99.3 6.14B9-BZAP 22.5 43.9 Mouse IgG2ak-Biotin 5.83 0.49 27.12E12-Biotin 202 96.8 9.1G12.8-Biotin 23.1 55.4 IgG2bk-BZAP 6.48 0.195 27.12E12-BZAP 268 98.8 9.1G12.8-BZAP 168 97.4

F. Example 6 TIM3-Specific Antibodies Reduce Cell Proliferation

The TIM3-specific antibodies were tested for ability to reduce cell proliferation of AML cells. TIM3-specific antibodies (or controls) were coated on plates at various concentrations for 2 hours, followed by addition of 10⁵ CMK cells. The cells were incubated at 37C in RPMI with 20% FBS for three days. FIG. 5 shows that the 1.7E10 and 7.10F6 antibodies, in particular, effectively inhibit AML cell growth.

The results indicate that cross-linking of the antibodies, e.g., by coating the antibodies on cell culture plates or beads, or mulimerizing antibodies into multivalent forms, improves the inhibition of cell growth.

G. Example 7 Complement Dependent Cytotoxicity (CDC) Activity of TIM3-Specific Antibodies

A subset of the TIM3-specific antibodies were tested for CDC activity. Human Fc chimeras were generated for the 1.7E10, 7.10F6, and 8.16C10 antibodies. Pfeiffer cells were incubated with human complement and the chimeric antibodies at various concentrations for 45 minutes. Specific lysis was determined by measuring the total number of live cells (see FIG. 6). All of the TIM3-specific chimeric antibodies tested were capable of mediating complement dependent cytotoxicity in a dose-dependent fashion.

H. Example 8 TIM3-Specific Antibodies Inhibit Release of Th1 Cytokines from Activated CD4+ T Cells

The TIM3-specific antibodies were tested for their effects on other cell types, namely CD4+ T cells. Fresh, purified PBMC were obtained from healthy donors, and isolated by Ficoll gradient. Naïve CD4+ T cells were isolated by negative selection. The CD4+ T cells were stimulated using CD3 and CD28 antibody-coated Dynabead® beads for 48 hours. TIM3-specific antibodies (or isotype controls) were added at the beginning of the culture at 5 ng/ml.

Following stimulation, Th1 cytokine levels, in particular, IL-6 and IFN-gamma, were tested by ELISA (using antibodies from eBioscience®). The results are shown in FIG. 7. Cytokine levels are shown relative to isotype controls, which are arbitrarily set at 1.0. Several of the TIM3-3 specific antibodies reduced the amount of inflammatory cytokine release from the activated T cells. For IFN-gamma, 1.7E10, 7.10F6, and 8.16C10 were particularly effective (>2-fold reduction compared to control). For IL-6, 8.16C10 and 9.1G12 were particularly effective (>2 fold reduction compared to control).

I. Example 9 TIM3 is Expressed on Solid Tumor Cells

A database of Affymetrix microarray gene expression studies indicated that TIM3 is expressed at an elevated level in certain solid tumor cells compared to normal, non-cancer cells of the same type. As expected, TIM3 was detected at a high frequency in AML and other hematopoietic cell cancer samples. Unexpectedly, a high level of TIM3 expression was also found at high frequency in the following diseased samples (number of samples showing HAVCR2 over-expression compared to control/number of samples analyzed).

Burkitt's lymphoma 4/4 Myleodysplastic syndrome 124/193 Chronic myelodysplastic syndrome 2/2 Hodgkin's lymphoma 5/5 Colon carcinoma 4/4 Ovarian carcinoma 4/4 Liver carcinoma 3/4 Prostate carcinoma 4/4 Uterine carcinoma 4/4 Breast carcinoma 4/4 Renal carcinoma 4/4

These results show that the TIM3 specific antibodies disclosed herein can be used to target solid tumor cells, as well as hematopoietic cancer cells for detection and/or therapy.

J. Example 10 TIM3-Specific Antibodies Bind AML Samples, but do not Bind CD34+ Cells from Normal Individuals

Using light scatter properties, blast and CD34+/38− populations were identified in the low side scatter population which constituted gate 1. Gate 2 was drawn around the cells identified by gate 1 that were still viable by propidium iodide. The merge of gate 1 and 2 constituted the live “blast” population. The CD34+/38− population was then identified from the live blast population which was labeled gate 3. The entire CD34+ population was gated rather than the CD34+/38−.

Table 6 shows number of samples that stained positive for TIM3 using the presently-disclosed antibodies, and the percentage of samples labeled. Positivity was determined by at least one TIM3-specific antibody staining by flow cytometry. Samples were broken down into FAB classification (M1-M5, or “Others” if not available) and by sample type (bone marrow BM or peripheral blood PB).

TABLE 6 Sample type TIM3 antibody binding All AML 25/56 (45%) M1  8/15 M2  7/13 M3 0/1 M4 6/9 M5 4/9 Others 0/9 BM 4/7 (57%) PB 21/49 (43%)

The TIM3-specific antibodies were individually tested for binding to CD34+ cells from a set of AML samples as shown in Table 7.

TABLE 7 Antibody 1.7E10.12 12E12 9.1G12 2E2 Positive/total 3/22 7/22 2/14 0/14

The staining characteristics were also determined for CD34+ cells from non-cancer (normal) individuals using the 1.7E10.12 and 12E12 TIM3-specific antibodies. Table 8 shows data from normal CD34+samples. Positivity was determined by flow cytometry against target clonal antibody. Number in each cell indicates MFI (% of cells positive). These data show that the presently disclosed TIM3-specific antibodies have a low likelihood of false positivity.

TABLE 8 1.7E10.12 12E12 Sample 1 1.72 (2.08%) 1.45 (4.41%) Sample 2 0.97 (0.88%) 1.02 (2.62%)

K. Example 11 Staining Characteristics of TIM3-Specific Antibodies on Other Hematological Malignancies

Binding of the TIM3-specific antibodies was also examined in leukemic and non-leukemic lymphomas. A variety of different subtypes of lymphomas were examined and of the 9 non-leukemic lymphomas tested, 3 were positive (33%). The striking finding was the higher probability of detectable occurrence of TIM3 in leukemic-phase lymphomas where 5 of the 6 samples tested were positive. This mirrored the cell line data collected from Daudi and Pfeiffer cell lines, generated from leukemic-phase lymphomas. Table 9 shows number of samples that stained positive by flow cytometry. Positivity was determined by staining by at least one TIM3-specific antibody. Samples were broken down into subtypes and solid vs leukemic phenotype.

TABLE 9 Hematological malignancy TIM3 positive Follicular 1/3 MCL 1/3 DLBCL 2/5 CLL/SLL 2/2 B-ALL 2/2 Non-leukemic 3/9 Leukemic 5/6

L. Example 12 TIM3-Specific Antibody Clone 12E12 has CDC Activity Against AML Cells from Patient Samples

Cells from AML patient samples were washed and dead cells removed using Live-Dead Kit (Miltenyi). Cells were resuspended to a final concentration of 0.8×10⁶/mL. 50 uL of the cell solution was added to each well of a black well, clear bottom 96-well plate (Costar). Two-fold stock antibody solutions (12E12) were prepared at a concentration of 20 ug/mL, 2 ug/mL, 200 ng/mL, 20 ng/mL or 2 ng/mL. 50 uL of the 2× antibody solution was added to each well containing cells allowing the final concentration in the wells to be 10 ug/mL, 1 ug/mL, 100 ng/mL, 10 ng/mL or 1 ng/mL. Cells and antibody were allowed to incubate for 10 minutes at room temperature prior to addition of baby rabbit complement. 1 mL of ice cold water was added to lyophilized complement (Cedarlane) and 10 uL was added to each cell+antibody solution well. Complement was also added to cells only as a cell+complement control. The plate was incubated at 37° C. for 2 hours before allowing to rest at room temperature for 10 minutes. Cell Titre-Glo (Promega) was prepared and 100 uL was added to each well and allowed to shake for 5-10 minutes prior to reading on a luminescent plate reader

Eleven AML samples with 12E12-detectable TIM3 expression were used to determine CDC activity of the antibody. FIG. 8A shows that 12E12 CDC activity does not depend on level of TIM3 expression. On the whole, a dose-dependent toxicity curve could be determined (see FIG. 8B, ms12E12). However, several samples seemed to have no CDC activity mediated by 12E12 (FIG. 8B, Insensitive). When the CDC data of those samples were removed, the remaining samples showed a steeper dose-dependent toxicity curve. Standard student t-test was used to identify non-sensitive samples to 12E12 by comparing wells with 12E12 treatment to IgG treatment. 

What is claimed is:
 1. An antibody linked to a cytotoxic agent, wherein the antibody specifically binds the extracellular domain of human T-cell Immunoglobulin Mucin (TIM) 3, wherein said binding results in internalization into a TIM3-expressing cell, and wherein the antibody is selected from the group consisting of (i) an antibody having light chain complementarity determining region (CDR) sequences of SEQ ID NOs:8-10 and heavy chain CDR sequences of SEQ ID NOs:3-5; (ii) an antibody having light chain CDR sequences of SEQ ID NOs:18-20 and heavy chain CDR sequences of SEQ ID NOs:13-15; (iii) an antibody having light chain CDR sequences of SEQ ID NOs:28-30 and heavy chain CDR sequences of SEQ ID NOs:23-25; (iv) an antibody having light chain CDR sequences of SEQ ID NOs:108-110 and heavy chain CDR sequences of SEQ ID NOs:103-105; and (v) an antibody having light chain CDR sequences of SEQ ID NOs:118-120 and heavy chain CDR sequences of SEQ ID NOs: 113-115.
 2. The antibody of claim 1, wherein the cytotoxic agent is selected from saporin, a taxane, a vinca alkaloid, an anthracycline, and cisplatin.
 3. The antibody of claim 1, wherein said TIM3-expressing cells are acute myeloid leukemia (AML) cells.
 4. The antibody of claim 1, wherein the TIM3-expressing cells are B lymphoma cells.
 5. The antibody of claim 1, wherein the antibody has light chain complementarity determining region (CDR) sequences of SEQ ID NOs:8-10 and heavy chain CDR sequences of SEQ ID NOs:3-5.
 6. The antibody of claim 1, wherein the antibody has light chain CDR sequences of SEQ ID NOs:18-20 and heavy chain CDR sequences of SEQ ID NOs:13-15.
 7. The antibody of claim 1, wherein the antibody has light chain CDR sequences of SEQ ID NOs:28-30 and heavy chain CDR sequences of SEQ ID NOs:23-25.
 8. The antibody of claim 1, wherein the antibody has light chain CDR sequences of SEQ ID NOs:108-110 and heavy chain CDR sequences of SEQ ID NOs:103-105.
 9. A pharmaceutical composition comprising the antibody of claim
 1. 